diff --git a/pkgs/native_assets_builder/test_data/wrong_build_output_3/hook/build.dart b/pkgs/native_assets_builder/test_data/wrong_build_output_3/hook/build.dart
index 454d60801..1e697f7ab 100644
--- a/pkgs/native_assets_builder/test_data/wrong_build_output_3/hook/build.dart
+++ b/pkgs/native_assets_builder/test_data/wrong_build_output_3/hook/build.dart
@@ -22,5 +22,5 @@ const _rightContents = '''{
   "encodedAssets": [],
   "dependencies": [],
   "metadata": {},
-  "version": "1.6.0"
+  "version": "1.7.0"
 }''';
diff --git a/pkgs/native_assets_cli/lib/src/code_assets/config.dart b/pkgs/native_assets_cli/lib/src/code_assets/config.dart
index f7a790439..b6d5ddd66 100644
--- a/pkgs/native_assets_cli/lib/src/code_assets/config.dart
+++ b/pkgs/native_assets_cli/lib/src/code_assets/config.dart
@@ -68,14 +68,22 @@ class CodeConfig {
   factory CodeConfig.fromJson(Map<String, Object?> json) {
     final dryRun = json.getOptional<bool>(_dryRunConfigKey) ?? false;
 
-    final linkModePreference =
-        LinkModePreference.fromString(json.string(_linkModePreferenceKey));
+    final linkModePreference = LinkModePreference.fromString(
+      json.code?.optionalString(_linkModePreferenceKey) ??
+          json.string(_linkModePreferenceKey),
+    );
     final targetArchitecture = dryRun
         ? null
-        : Architecture.fromString(json.string(_targetArchitectureKey,
-            validValues: Architecture.values.map((a) => a.name)));
-    final targetOS = OS.fromString(json.string(_targetOSConfigKey));
-    final cCompiler = switch (json.optionalMap(_compilerKey)) {
+        : Architecture.fromString(json.code?.optionalString(
+                _targetArchitectureKey,
+                validValues: Architecture.values.map((a) => a.name)) ??
+            json.string(_targetArchitectureKey,
+                validValues: Architecture.values.map((a) => a.name)));
+    final targetOS = OS.fromString(
+        json.code?.optionalString(_targetOSConfigKey) ??
+            json.string(_targetOSConfigKey));
+    final cCompiler = switch (json.code?.optionalMap(_compilerKey) ??
+        json.optionalMap(_compilerKey)) {
       final Map<String, Object?> map => CCompilerConfig.fromJson(map),
       null => null
     };
@@ -151,8 +159,12 @@ class IOSConfig {
         _targetVersion = targetVersion;
 
   IOSConfig.fromJson(Map<String, Object?> json)
-      : _targetVersion = json.optionalInt(_targetIOSVersionKey),
-        _targetSdk = switch (json.optionalString(_targetIOSSdkKey)) {
+      : _targetVersion =
+            json.code?.optionalMap(_iosKey)?.optionalInt(_targetVersionKey) ??
+                json.optionalInt(_targetIOSVersionKeyDeprecated),
+        _targetSdk = switch (
+            json.code?.optionalMap(_iosKey)?.optionalString(_targetSdkKey) ??
+                json.optionalString(_targetIOSSdkKeyDeprecated)) {
           null => null,
           String e => IOSSdk.fromString(e)
         };
@@ -176,7 +188,10 @@ class AndroidConfig {
   }) : _targetNdkApi = targetNdkApi;
 
   AndroidConfig.fromJson(Map<String, Object?> json)
-      : _targetNdkApi = json.optionalInt(_targetAndroidNdkApiKey);
+      : _targetNdkApi = json.code
+                ?.optionalMap(_androidKey)
+                ?.optionalInt(_targetNdkApiKey) ??
+            json.optionalInt(_targetAndroidNdkApiKeyDeprecated);
 }
 
 extension AndroidConfigSyntactic on AndroidConfig {
@@ -195,7 +210,9 @@ class MacOSConfig {
   }) : _targetVersion = targetVersion;
 
   MacOSConfig.fromJson(Map<String, Object?> json)
-      : _targetVersion = json.optionalInt(_targetMacOSVersionKey);
+      : _targetVersion =
+            json.code?.optionalMap(_macosKey)?.optionalInt(_targetVersionKey) ??
+                json.optionalInt(_targetMacOSVersionKeyDeprecated);
 }
 
 extension MacOSConfigSyntactic on MacOSConfig {
@@ -258,22 +275,45 @@ extension CodeAssetBuildInputBuilder on HookConfigBuilder {
   }) {
     if (targetArchitecture != null) {
       json[_targetArchitectureKey] = targetArchitecture.toString();
+      json.setNested([_configKey, _codeKey, _targetArchitectureKey],
+          targetArchitecture.toString());
     }
     json[_targetOSConfigKey] = targetOS.toString();
+    json.setNested(
+        [_configKey, _codeKey, _targetOSConfigKey], targetOS.toString());
     json[_linkModePreferenceKey] = linkModePreference.toString();
+    json.setNested([_configKey, _codeKey, _linkModePreferenceKey],
+        linkModePreference.toString());
     if (cCompiler != null) {
       json[_compilerKey] = cCompiler.toJson();
+      json.setNested([_configKey, _codeKey, _compilerKey], cCompiler.toJson());
     }
 
     // Note, using ?. instead of !. makes missing data be a semantic error
     // rather than a syntactic error to be caught in the validation.
     if (targetOS == OS.android) {
-      json[_targetAndroidNdkApiKey] = android?.targetNdkApi;
+      json[_targetAndroidNdkApiKeyDeprecated] = android?.targetNdkApi;
+      json.setNested(
+        [_configKey, _codeKey, _androidKey, _targetNdkApiKey],
+        android?.targetNdkApi,
+      );
     } else if (targetOS == OS.iOS) {
-      json[_targetIOSSdkKey] = iOS?.targetSdk.toString();
-      json[_targetIOSVersionKey] = iOS?.targetVersion;
+      json[_targetIOSSdkKeyDeprecated] = iOS?.targetSdk.toString();
+      json[_targetIOSVersionKeyDeprecated] = iOS?.targetVersion;
+      json.setNested(
+        [_configKey, _codeKey, _iosKey, _targetSdkKey],
+        iOS?.targetSdk.toString(),
+      );
+      json.setNested(
+        [_configKey, _codeKey, _iosKey, _targetVersionKey],
+        iOS?.targetVersion,
+      );
     } else if (targetOS == OS.macOS) {
-      json[_targetMacOSVersionKey] = macOS?.targetVersion;
+      json[_targetMacOSVersionKeyDeprecated] = macOS?.targetVersion;
+      json.setNested(
+        [_configKey, _codeKey, _macosKey, _targetVersionKey],
+        macOS?.targetVersion,
+      );
     }
   }
 }
@@ -298,11 +338,25 @@ extension CodeAssetLinkOutput on LinkOutputAssets {
 
 const String _compilerKey = 'c_compiler';
 const String _linkModePreferenceKey = 'link_mode_preference';
-const String _targetAndroidNdkApiKey = 'target_android_ndk_api';
+const String _targetNdkApiKey = 'target_ndk_api';
+const String _targetAndroidNdkApiKeyDeprecated = 'target_android_ndk_api';
 const String _targetArchitectureKey = 'target_architecture';
-const String _targetIOSSdkKey = 'target_ios_sdk';
-const String _targetIOSVersionKey = 'target_ios_version';
-const String _targetMacOSVersionKey = 'target_macos_version';
+const String _targetSdkKey = 'target_sdk';
+const String _targetIOSSdkKeyDeprecated = 'target_ios_sdk';
+const String _targetVersionKey = 'target_version';
+const String _targetIOSVersionKeyDeprecated = 'target_ios_version';
+const String _targetMacOSVersionKeyDeprecated = 'target_macos_version';
 const String _targetOSConfigKey = 'target_os';
 
 const _dryRunConfigKey = 'dry_run';
+
+const _configKey = 'config';
+const _codeKey = 'code';
+const _androidKey = 'android';
+const _iosKey = 'ios';
+const _macosKey = 'macos';
+
+extension on Map<String, Object?> {
+  Map<String, Object?>? get code =>
+      optionalMap(_configKey)?.optionalMap(_codeKey);
+}
diff --git a/pkgs/native_assets_cli/lib/src/config.dart b/pkgs/native_assets_cli/lib/src/config.dart
index a9ec3324d..c6eea6310 100644
--- a/pkgs/native_assets_cli/lib/src/config.dart
+++ b/pkgs/native_assets_cli/lib/src/config.dart
@@ -104,18 +104,9 @@ sealed class HookInputBuilder {
   /// [BuildInput] being built with this [BuildInputBuilder]. It is therefore
   /// assumed the output directory has not been set yet.
   String computeChecksum() {
-    if (json.containsKey(_outDirInputKey) ||
-        json.containsKey(_outDirSharedInputKey) ||
-        json.containsKey(_assetsKey)) {
-      // The bundling tools would first calculate the checksum, create an output
-      // directory and then call [setupHookInput].
-      // The output directory should not depend on the assets passed in for
-      // linking.
-      throw StateError('The checksum should be generated before setting '
-          'up the hook configuration');
-    }
+    final config = json[_configKey];
     final hash = sha256
-        .convert(const JsonEncoder().fuse(const Utf8Encoder()).convert(json))
+        .convert(const JsonEncoder().fuse(const Utf8Encoder()).convert(config))
         .toString()
         // 256 bit hashes lead to 64 hex character strings.
         // To avoid overflowing file paths limits, only use 32.
@@ -137,6 +128,8 @@ const _packageRootInputKey = 'package_root';
 const _supportedAssetTypesKey = 'supported_asset_types';
 const _buildAssetTypesKey = 'build_asset_types';
 
+const _configKey = 'config';
+
 final class BuildInput extends HookInput {
   final Map<String, Metadata> metadata;
 
@@ -179,6 +172,7 @@ final class HookConfigBuilder {
   }) {
     json[_buildAssetTypesKey] = buildAssetTypes;
     json[_supportedAssetTypesKey] = buildAssetTypes;
+    json.setNested([_configKey, _buildAssetTypesKey], buildAssetTypes);
   }
 }
 
@@ -193,6 +187,7 @@ extension BuildConfigBuilderSetup on BuildConfigBuilder {
   }) {
     json[_dryRunConfigKey] = dryRun;
     json[_linkingEnabledKey] = linkingEnabled;
+    json.setNested([_configKey, _linkingEnabledKey], linkingEnabled);
 
     // TODO: Bump min-SDK constraint to 3.7 and remove once stable.
     if (!dryRun) {
@@ -583,7 +578,7 @@ extension type EncodedAssetLinkOutputBuilder._(LinkOutputBuilder _builder) {
 ///
 /// We'll never bump the major version. Removing old keys from the input and
 /// output is done via modifying [latestParsableVersion].
-final latestVersion = Version(1, 6, 0);
+final latestVersion = Version(1, 7, 0);
 
 /// The parser can deal with inputs and outputs down to this version.
 ///
@@ -607,7 +602,10 @@ final class HookConfig {
   final List<String> buildAssetTypes;
 
   HookConfig(this.json)
-      : buildAssetTypes = json.optionalStringList(_buildAssetTypesKey) ??
+      : buildAssetTypes = json
+                .optionalMap(_configKey)
+                ?.optionalStringList(_buildAssetTypesKey) ??
+            json.optionalStringList(_buildAssetTypesKey) ??
             json.optionalStringList(_supportedAssetTypesKey) ??
             const [];
 }
@@ -627,5 +625,7 @@ final class BuildConfig extends HookConfig {
   BuildConfig(super.json)
       // ignore: deprecated_member_use_from_same_package
       : dryRun = json.getOptional<bool>(_dryRunConfigKey) ?? false,
-        linkingEnabled = json.get<bool>(_linkingEnabledKey);
+        linkingEnabled =
+            json.optionalMap(_configKey)?.optionalBool(_linkingEnabledKey) ??
+                json.get<bool>(_linkingEnabledKey);
 }
diff --git a/pkgs/native_assets_cli/lib/src/json_utils.dart b/pkgs/native_assets_cli/lib/src/json_utils.dart
index c267b86c7..4533697f3 100644
--- a/pkgs/native_assets_cli/lib/src/json_utils.dart
+++ b/pkgs/native_assets_cli/lib/src/json_utils.dart
@@ -16,7 +16,15 @@ extension MapJsonUtils on Map<String, Object?> {
     return value;
   }
 
-  String? optionalString(String key) => getOptional<String>(key);
+  String? optionalString(String key, {Iterable<String>? validValues}) {
+    final value = getOptional<String>(key);
+    if (value == null) return null;
+    if (validValues != null && !validValues.contains(value)) {
+      throw FormatException('Json "$key" had value $value but expected one of '
+          '${validValues.join(',')}');
+    }
+    return value;
+  }
 
   bool? optionalBool(String key) => getOptional<bool>(key);
   core.int int(String key) => get<core.int>(key);
@@ -62,6 +70,14 @@ extension MapJsonUtils on Map<String, Object?> {
         'Unexpected value \'$value\' for key \'.$key\' in input file. '
         'Expected a $T?.');
   }
+
+  void setNested(List<String> nestedMapKeys, Object? value) {
+    var map = this;
+    for (final key in nestedMapKeys.sublist(0, nestedMapKeys.length - 1)) {
+      map = (map[key] ??= <String, Object?>{}) as Map<String, Object?>;
+    }
+    map[nestedMapKeys.last] = value;
+  }
 }
 
 extension ListJsonUtils on List<Object?> {
diff --git a/pkgs/native_assets_cli/test/build_config_test.dart b/pkgs/native_assets_cli/test/build_config_test.dart
index 497d8e466..815f6d41f 100644
--- a/pkgs/native_assets_cli/test/build_config_test.dart
+++ b/pkgs/native_assets_cli/test/build_config_test.dart
@@ -56,6 +56,10 @@ void main() async {
     final expectedInputJson = {
       'build_asset_types': ['my-asset-type'],
       'build_mode': 'release',
+      'config': {
+        'build_asset_types': ['my-asset-type'],
+        'linking_enabled': false,
+      },
       'dependency_metadata': {
         'bar': {
           'key': 'value',
@@ -108,6 +112,10 @@ void main() async {
 
     final expectedInputJson = {
       'build_asset_types': ['my-asset-type'],
+      'config': {
+        'build_asset_types': ['my-asset-type'],
+        'linking_enabled': true,
+      },
       'dependency_metadata': <String, Object?>{},
       'dry_run': true,
       'linking_enabled': true,
diff --git a/pkgs/native_assets_cli/test/build_output_test.dart b/pkgs/native_assets_cli/test/build_output_test.dart
index 58b73b2f5..39d4cd481 100644
--- a/pkgs/native_assets_cli/test/build_output_test.dart
+++ b/pkgs/native_assets_cli/test/build_output_test.dart
@@ -49,7 +49,7 @@ void main() {
 
     // The JSON format of the build output.
     <String, Object?>{
-      'version': '1.6.0',
+      'version': '1.7.0',
       'dependencies': ['path0', 'path1', 'path2'],
       'metadata': {
         'meta-a': 'meta-b',
diff --git a/pkgs/native_assets_cli/test/checksum_test.dart b/pkgs/native_assets_cli/test/checksum_test.dart
index 534254b8a..9d5b66ef9 100644
--- a/pkgs/native_assets_cli/test/checksum_test.dart
+++ b/pkgs/native_assets_cli/test/checksum_test.dart
@@ -2,8 +2,6 @@
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
-import 'dart:convert';
-
 import 'package:native_assets_cli/code_assets_builder.dart';
 import 'package:native_assets_cli/data_assets_builder.dart';
 import 'package:test/test.dart';
@@ -13,40 +11,73 @@ import 'helpers.dart';
 void main() {
   test('checksum', () async {
     // metadata, cc, link vs build, metadata, haslink
-    final inputs = <String>[];
+
     final checksums = <String>[];
+    final inputs = <String, Object?>{};
 
-    for (final dryRun in [true, false]) {
-      for (final linking in [true, false]) {
-        for (final assetType in [CodeAsset.type, DataAsset.type]) {
+    for (final hook in ['build', 'link']) {
+      for (final linking in [true, if (hook == 'build') false]) {
+        for (final assetTypes in [
+          [CodeAsset.type],
+          [CodeAsset.type, DataAsset.type],
+          [DataAsset.type],
+        ]) {
           for (final os in [
-            OS.linux,
-            if (assetType == CodeAsset.type) OS.macOS,
+            OS.android,
+            if (assetTypes.contains(CodeAsset.type)) OS.iOS,
+            if (assetTypes.contains(CodeAsset.type)) OS.macOS,
           ]) {
             for (final architecture in [
               Architecture.arm64,
-              if (assetType == CodeAsset.type) Architecture.x64,
+              if (assetTypes.contains(CodeAsset.type)) Architecture.x64,
             ]) {
-              final builder = BuildInputBuilder()
-                ..config.setupBuild(
-                  dryRun: dryRun,
-                  linkingEnabled: linking,
-                );
-              builder.config.setupShared(buildAssetTypes: [assetType]);
-              if (assetType == CodeAsset.type) {
-                builder.config.setupCode(
-                  targetArchitecture: architecture,
-                  targetOS: os,
-                  macOS: os == OS.macOS
-                      ? MacOSConfig(targetVersion: defaultMacOSVersion)
-                      : null,
-                  linkModePreference: LinkModePreference.dynamic,
-                );
+              for (final targetVersion in [
+                if (os == OS.android) 30,
+                if (os == OS.iOS) flutteriOSHighestBestEffort,
+                if (os == OS.iOS) flutteriOSHighestSupported,
+                if (os == OS.macOS) defaultMacOSVersion,
+              ]) {
+                for (final iOSSdk in [
+                  if (architecture == Architecture.arm64 && os == OS.iOS)
+                    IOSSdk.iPhoneOS,
+                  IOSSdk.iPhoneSimulator,
+                ]) {
+                  final builder = BuildInputBuilder();
+                  if (hook == 'build') {
+                    builder.config.setupBuild(
+                      dryRun: false, // no embedders will pass true anymore
+                      linkingEnabled: linking,
+                    );
+                  }
+                  builder.config.setupShared(buildAssetTypes: assetTypes);
+                  if (assetTypes.contains(CodeAsset.type)) {
+                    builder.config.setupCode(
+                      targetArchitecture: architecture,
+                      targetOS: os,
+                      android: os == OS.android
+                          ? AndroidConfig(targetNdkApi: targetVersion)
+                          : null,
+                      macOS: os == OS.macOS
+                          ? MacOSConfig(targetVersion: targetVersion)
+                          : null,
+                      iOS: os == OS.iOS
+                          ? IOSConfig(
+                              targetVersion: targetVersion,
+                              targetSdk: iOSSdk,
+                            )
+                          : null,
+                      linkModePreference: LinkModePreference.dynamic,
+                    );
+                  }
+                  final checksum = builder.computeChecksum();
+                  checksums.add(checksum);
+
+                  if (inputs[checksum] != null) {
+                    expect(builder.json['config'], inputs[checksum]);
+                  }
+                  inputs[checksum] = builder.json['config'];
+                }
               }
-              inputs.add(
-                const JsonEncoder.withIndent(' ').convert(builder.json),
-              );
-              checksums.add(builder.computeChecksum());
             }
           }
         }
@@ -61,26 +92,69 @@ void main() {
     // needing to update this list).
 
     final expectedChecksums = <String>[
-      '079353bf7f09a5a78aad5dfb74d160ce',
-      '3f77f197abd56950f6878720f40f1d78',
-      '95afb0b082567b75143a5a3fe23ded7f',
-      '20a82fc01786d82ec2e70c81e384ca53',
-      '9b4a6923ab07618074631e9ee8ea5451',
-      '1ba05dccc6b7d760f2c085dfb3b3e9be',
-      '86ca6c0d669baa2f0d29b81aa9db65d9',
-      'ad261f0ea9c06e69eaf9870161da902f',
-      '4973835d48a96917eb2b4fe3266c60f4',
-      '1c4bddfe0111033df5fd1903123a759b',
-      '07d32fc26a66558589bd2ef3d243a1bf',
-      '6237121ffae0bb44b6489913f859e595',
-      '5ab1d45dc1b8365df17dc13bfe725e3e',
-      'efff82f6321e8f2ad2d83f7b87890d12',
-      '9939ebdbc70de2750b26857ccdf7a308',
-      '2ac3ed117b93db3686b51c8d3da6947d',
-      '47d6a16f82e7dc71156af0578e1cde4c',
-      '07eaf868dd64ef1ffd717111d7a73263',
-      '5df468122615987a0daa4da40c3f4e07',
-      '0e551c890758631dfc1dd549d8278fc8',
+      '24ccf8d332a8c8d55e476dc3c6bc583b',
+      '7f36bc59f947abd6af6cee575138e754',
+      'd0aba834036fead9bab453d527eae4ed',
+      '1ceb39975433d22ece4a862af5ebc13e',
+      '92a29907211743f4dfa05214efca2f5b',
+      '43579d544a56d1c2f41324690122e16f',
+      'd88c23a4c520275ed03e9b8edee48674',
+      '2765b39d6a39e71712109588acf05c03',
+      '66a6f953369ef21ee2576e4e3fde3ad3',
+      '611a7687747e116ddcc7e50d8ac079d4',
+      'c92a32ed941614b8343197d1d42fa27e',
+      '7498ff7cbb07d9d2dd127377b30f26fa',
+      '5c0a592096625690802ac0671f4034e0',
+      '65e125ee71ea5fe4bc79d54003cab931',
+      '790b552e75a98b90a77455da90c1ea87',
+      '98fba8ecfc7dd07c798503dfc87da0bb',
+      '7784fdf4afe8b22c017c5d3f7983777b',
+      'eff20a22ed0e429fa20c1458a2c1f0b8',
+      'c4b179cfd16d663ae58bd1a06618d23b',
+      'd31c785c41b9d852aef30251a46bf214',
+      'a89fc3d8de5647d6825b47592e5dd7b5',
+      'f13c6adb12346391761a9e0fcfa37568',
+      '887b0c294956ffe456687778a80913f7',
+      'c0cb2fe6ed8f7bc27d0fb166a139c31e',
+      'c51f6b56cd8083e2e6d9d5db2997c7fd',
+      '9ccb0b5e6f39d3655f7ef2cb1b3f02b7',
+      '440a909a495e1445cc89392176fceec8',
+      '99e61d87aaaba64b91cedffcb50c521b',
+      'f0150c4470ef8e9917d1f500b60f0a8b',
+      'bce703d4756f1345959d99f371f70be7',
+      'c24f96a671ac4320163ba6ad01e08c22',
+      '4813128ab93a41cf6a2ba92e1ac87bd8',
+      '6b8f417d14bdc9cdda90122dc2e16ca4',
+      '306ae22675d94f717eb58db9bfd7ac14',
+      'b4c4531503bd3f814367e78081f183f2',
+      'c5903374f46c510508f9d6314ac82c2d',
+      'd5bf990a551941d29309dbdd26c0cdf1',
+      'e773863012e1cea85b39134357c12c45',
+      '36eb9110b66f57866c565495fa145f02',
+      'b527b041d448d9d3938391348b2b296d',
+      '9f9a66ee78bdec8e4dab4a63029dbde3',
+      '0376b13decbf88bc0901b7c853f76bb0',
+      '527bbf58f698036f78b5519553186d0f',
+      '8e937a8834d9fcb697b5a3c80ac04dd0',
+      '4358d31df880c53face01c18945fa14b',
+      '518e6a0bed957d3e5e88a18a44532ca2',
+      '614152ce8d7b591916d78838711b75f9',
+      '0f89f3db1d379ec581b4e896f5060d0a',
+      'f7a554031e353366b157d5af0a774bf8',
+      'a96c3052f878d4d08585b640ea77970e',
+      '7c3f0134505f73c91825ea837f1e885e',
+      '575b6bd07de1a3fdb150b7626526bd47',
+      'ecdfaaa2f4bc2708375e6e6a980578a8',
+      '06c509e166c7fa7d8ac8c56806da53ba',
+      'dfb39e5ac164e4f269fb7e9ae084a2a4',
+      '1b3cbac826b58a001e3ed7539f55f652',
+      '6fbc5b8630c3d27abf3a810051dd9271',
+      '43025538d82ed0492a5928aefb0767ab',
+      '0172735fa45b76ec9f8c3a0416608721',
+      '547dfca0aa25ffa8e68ae1218c19b339',
+      '19e984d77d877f7d5a20eb8fe523bee6',
+      '5f644023cc187fe71f01daccc9bdbe76',
+      'bbdaf85e3a026c0bd87a56e7102a6beb',
     ];
     printOnFailure('final expectedChecksums = <String>[');
     printOnFailure(checksums.map((e) => "  '$e',").join('\n'));
@@ -90,3 +164,6 @@ void main() {
     }
   });
 }
+
+const flutteriOSHighestBestEffort = 16;
+const flutteriOSHighestSupported = 17;
diff --git a/pkgs/native_assets_cli/test/code_assets/config_test.dart b/pkgs/native_assets_cli/test/code_assets/config_test.dart
index 5f0859a64..85fa79b41 100644
--- a/pkgs/native_assets_cli/test/code_assets/config_test.dart
+++ b/pkgs/native_assets_cli/test/code_assets/config_test.dart
@@ -58,30 +58,93 @@ void main() async {
     expect(codeConfig.cCompiler, null);
   }
 
-  void expectCorrectCodeConfig(
-      Map<String, Object?> json, CodeConfig codeConfig) {
-    <String, Object?>{
-      'build_asset_types': [CodeAsset.type],
-      'link_mode_preference': 'prefer-static',
-      'target_android_ndk_api': 30,
-      'target_architecture': 'arm64',
-      'c_compiler': {
-        'ar': fakeAr.toFilePath(),
-        'ld': fakeLd.toFilePath(),
-        'cc': fakeClang.toFilePath(),
-        'env_script': fakeVcVars.toFilePath(),
-        'env_script_arguments': ['arg0', 'arg1'],
-      },
-    }.forEach((k, v) {
-      expect(json[k], v);
-    });
+  // Full JSON to see where the config sits in the full JSON.
+  // When removing the non-hierarchical JSON, we can change this test to only
+  // check the nested key.
+  Map<String, Object> inputJson({
+    String hookType = 'build',
+    bool includeDeprecated = true,
+    OS targetOS = OS.android,
+  }) =>
+      {
+        if (hookType == 'link')
+          'assets': [
+            {
+              'architecture': 'riscv64',
+              'file': 'not there',
+              'id': 'package:my_package/name',
+              'link_mode': {'type': 'dynamic_loading_bundle'},
+              'os': 'android',
+              'type': 'native_code'
+            }
+          ],
+        if (includeDeprecated) 'build_asset_types': [CodeAsset.type],
+        if (includeDeprecated) 'build_mode': 'release',
+        'config': {
+          'build_asset_types': ['native_code'],
+          if (hookType == 'build') 'linking_enabled': false,
+          'code': {
+            'target_architecture': 'arm64',
+            'target_os': targetOS.name,
+            'link_mode_preference': 'prefer-static',
+            'c_compiler': {
+              'ar': fakeAr.toFilePath(),
+              'ld': fakeLd.toFilePath(),
+              'cc': fakeClang.toFilePath(),
+              'env_script': fakeVcVars.toFilePath(),
+              'env_script_arguments': ['arg0', 'arg1'],
+            },
+            if (targetOS == OS.android) 'android': {'target_ndk_api': 30},
+            if (targetOS == OS.macOS) 'macos': {'target_version': 13},
+            if (targetOS == OS.iOS)
+              'ios': {
+                'target_sdk': 'iphoneos',
+                'target_version': 13,
+              },
+          },
+        },
+        if (includeDeprecated)
+          'c_compiler': {
+            'ar': fakeAr.toFilePath(),
+            'ld': fakeLd.toFilePath(),
+            'cc': fakeClang.toFilePath(),
+            'env_script': fakeVcVars.toFilePath(),
+            'env_script_arguments': ['arg0', 'arg1'],
+          },
+        if (hookType == 'build' && includeDeprecated) 'dry_run': false,
+        if (hookType == 'build' && includeDeprecated) 'linking_enabled': false,
+        if (includeDeprecated) 'link_mode_preference': 'prefer-static',
+        'out_dir_shared': outputDirectoryShared.toFilePath(),
+        'out_dir': outDirUri.toFilePath(),
+        'package_name': packageName,
+        'package_root': packageRootUri.toFilePath(),
+        if (includeDeprecated) 'supported_asset_types': [CodeAsset.type],
+        if (includeDeprecated && targetOS == OS.android)
+          'target_android_ndk_api': 30,
+        if (includeDeprecated) 'target_architecture': 'arm64',
+        if (includeDeprecated) 'target_os': targetOS.name,
+        'version': '1.7.0',
+      };
 
-    expect(codeConfig.targetArchitecture, Architecture.arm64);
-    expect(codeConfig.android.targetNdkApi, 30);
-    expect(codeConfig.linkModePreference, LinkModePreference.preferStatic);
-    expect(codeConfig.cCompiler?.compiler, fakeClang);
-    expect(codeConfig.cCompiler?.linker, fakeLd);
-    expect(codeConfig.cCompiler?.archiver, fakeAr);
+  void expectCorrectCodeConfig(
+    CodeConfig codeCondig, {
+    OS targetOS = OS.android,
+  }) {
+    expect(codeCondig.targetArchitecture, Architecture.arm64);
+    if (targetOS == OS.android) {
+      expect(codeCondig.android.targetNdkApi, 30);
+    }
+    if (targetOS == OS.macOS) {
+      expect(codeCondig.macOS.targetVersion, 13);
+    }
+    if (targetOS == OS.iOS) {
+      expect(codeCondig.iOS.targetVersion, 13);
+      expect(codeCondig.iOS.targetSdk, IOSSdk.iPhoneOS);
+    }
+    expect(codeCondig.linkModePreference, LinkModePreference.preferStatic);
+    expect(codeCondig.cCompiler?.compiler, fakeClang);
+    expect(codeCondig.cCompiler?.linker, fakeLd);
+    expect(codeCondig.cCompiler?.archiver, fakeAr);
   }
 
   test('BuildInput.config.code (dry-run)', () {
@@ -135,7 +198,26 @@ void main() async {
         ),
       );
     final input = BuildInput(inputBuilder.json);
-    expectCorrectCodeConfig(input.json, input.config.code);
+    expect(input.json, inputJson());
+    expectCorrectCodeConfig(input.config.code);
+  });
+
+  test('BuildInput from json without deprecated keys', () {
+    for (final targetOS in [OS.android, OS.iOS, OS.macOS]) {
+      final input = BuildInput(inputJson(
+        includeDeprecated: false,
+        targetOS: targetOS,
+      ));
+      expect(input.packageName, packageName);
+      expect(input.packageRoot, packageRootUri);
+      expect(input.outputDirectory, outDirUri);
+      expect(input.outputDirectoryShared, outputDirectoryShared);
+      expect(input.config.linkingEnabled, false);
+      // ignore: deprecated_member_use_from_same_package
+      expect(input.config.dryRun, false);
+      expect(input.config.buildAssetTypes, [CodeAsset.type]);
+      expectCorrectCodeConfig(input.config.code, targetOS: targetOS);
+    }
   });
 
   test('LinkInput.{code,codeAssets}', () {
@@ -165,10 +247,27 @@ void main() async {
         ),
       );
     final input = LinkInput(inputBuilder.json);
-    expectCorrectCodeConfig(input.json, input.config.code);
+    expect(input.json, inputJson(hookType: 'link'));
+    expectCorrectCodeConfig(input.config.code);
     expect(input.assets.encodedAssets, assets);
   });
 
+  test('LinkInput from json without deprecated keys', () {
+    for (final targetOS in [OS.android, OS.iOS, OS.macOS]) {
+      final input = LinkInput(inputJson(
+        includeDeprecated: false,
+        targetOS: targetOS,
+        hookType: 'link',
+      ));
+      expect(input.packageName, packageName);
+      expect(input.packageRoot, packageRootUri);
+      expect(input.outputDirectory, outDirUri);
+      expect(input.outputDirectoryShared, outputDirectoryShared);
+      expect(input.config.buildAssetTypes, [CodeAsset.type]);
+      expectCorrectCodeConfig(input.config.code, targetOS: targetOS);
+    }
+  });
+
   test('BuildInput.config.code: invalid architecture', () {
     final input = {
       'dry_run': false,
diff --git a/pkgs/native_assets_cli/test/link_config_test.dart b/pkgs/native_assets_cli/test/link_config_test.dart
index 2d951f82c..acc9e430e 100644
--- a/pkgs/native_assets_cli/test/link_config_test.dart
+++ b/pkgs/native_assets_cli/test/link_config_test.dart
@@ -47,6 +47,9 @@ void main() async {
       'assets': [for (final asset in assets) asset.toJson()],
       'build_asset_types': ['asset-type-1', 'asset-type-2'],
       'build_mode': 'release',
+      'config': {
+        'build_asset_types': ['asset-type-1', 'asset-type-2'],
+      },
       'out_dir_shared': outputDirectoryShared.toFilePath(),
       'out_dir': outDirUri.toFilePath(),
       'package_name': packageName,
diff --git a/pkgs/native_assets_cli/test/link_output_test.dart b/pkgs/native_assets_cli/test/link_output_test.dart
index 34de1c2b9..9bd28313d 100644
--- a/pkgs/native_assets_cli/test/link_output_test.dart
+++ b/pkgs/native_assets_cli/test/link_output_test.dart
@@ -35,7 +35,7 @@ void main() {
 
     // The JSON format of the link output.
     <String, Object?>{
-      'version': '1.6.0',
+      'version': '1.7.0',
       'dependencies': ['path0', 'path1', 'path2'],
       'assets': [
         {'a-0': 'v-0', 'type': 'my-asset-type'},