diff --git a/CHANGELOG.md b/CHANGELOG.md
index b804937b0..23111cd7f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@
 - Workaround Swift shorthand if-let syntax bug (https://github.com/apple/swift/issues/61509). Global properties are not handled by this workaround.
 - Fix retaining inferred associated types.
 - Fix redundant public accessibility analysis for types used in closure signatures.
+- Conflicting index store units are now detected and result in an error.
 
 ## 2.10.0 (2022-10-10)
 
diff --git a/Package.resolved b/Package.resolved
index d8db9bc73..e2c54cc61 100644
--- a/Package.resolved
+++ b/Package.resolved
@@ -39,11 +39,11 @@
       },
       {
         "package": "SwiftIndexStore",
-        "repositoryURL": "https://github.com/kateinoigakukun/swift-indexstore",
+        "repositoryURL": "https://github.com/ileitch/swift-indexstore",
         "state": {
           "branch": null,
-          "revision": "ea41d13796dbbc4dc36d97ba5edb20a021aaf4e4",
-          "version": "0.1.5"
+          "revision": "f4e55301ca7d6d25057c514bea0e7407a1620f5f",
+          "version": null
         }
       },
       {
diff --git a/Package.swift b/Package.swift
index 1ecab8e8c..f10e063e3 100644
--- a/Package.swift
+++ b/Package.swift
@@ -6,7 +6,7 @@ var dependencies: [Package.Dependency] = [
     .package(url: "https://github.com/jpsim/Yams", from: "5.0.0"),
     .package(url: "https://github.com/tadija/AEXML", from: "4.0.0"),
     .package(url: "https://github.com/apple/swift-argument-parser", from: "1.0.0"),
-    .package(name: "SwiftIndexStore", url: "https://github.com/kateinoigakukun/swift-indexstore", from: "0.0.0"),
+    .package(name: "SwiftIndexStore", url: "https://github.com/ileitch/swift-indexstore", .revision("f4e55301ca7d6d25057c514bea0e7407a1620f5f")),
     .package(name: "SwiftSyntax", url: "https://github.com/apple/swift-syntax.git", .revision("a82041008d2c678a97407fbd0ce420d3ab047538"))
 ]
 
diff --git a/Sources/PeripheryKit/Indexer/SwiftIndexer.swift b/Sources/PeripheryKit/Indexer/SwiftIndexer.swift
index c08a03511..3b84f70ec 100644
--- a/Sources/PeripheryKit/Indexer/SwiftIndexer.swift
+++ b/Sources/PeripheryKit/Indexer/SwiftIndexer.swift
@@ -75,7 +75,11 @@ public final class SwiftIndexer {
         let jobs = try unitsByFile.map { (file, units) -> Job in
             let modules = try units.reduce(into: Set<String>()) { (set, unit) in
                 if let name = try indexStore.moduleName(for: unit) {
-                    set.insert(name)
+                    let (didInsert, _) = set.insert(name)
+                    if !didInsert {
+                        let targets = try Set(units.compactMap { try indexStore.target(for: $0) })
+                        throw PeripheryError.conflictingIndexUnitsError(file: file, module: name, unitTargets: targets)
+                    }
                 }
             }
             let sourceFile = SourceFile(path: file, modules: modules)
diff --git a/Sources/Shared/PeripheryError.swift b/Sources/Shared/PeripheryError.swift
index 3bea79bf4..002840da3 100644
--- a/Sources/Shared/PeripheryError.swift
+++ b/Sources/Shared/PeripheryError.swift
@@ -1,4 +1,5 @@
 import Foundation
+import SystemPackage
 
 public enum PeripheryError: Error, LocalizedError, CustomStringConvertible {
     case shellCommandFailed(cmd: String, args: [String], status: Int32, output: String)
@@ -20,6 +21,7 @@ public enum PeripheryError: Error, LocalizedError, CustomStringConvertible {
     case unindexedTargetsError(targets: Set<String>, indexStorePath: String)
     case jsonDeserializationError(error: Error, json: String)
     case indexStoreNotFound(derivedDataPath: String)
+    case conflictingIndexUnitsError(file: FilePath, module: String, unitTargets: Set<String>)
 
     public var errorDescription: String? {
         switch self {
@@ -68,6 +70,13 @@ public enum PeripheryError: Error, LocalizedError, CustomStringConvertible {
             return "JSON deserialization failed: \(describe(error))\nJSON:\n\(json)"
         case let .indexStoreNotFound(derivedDataPath):
             return "Failed to find index datastore at path: \(derivedDataPath)"
+        case let .conflictingIndexUnitsError(file, module, targets):
+            var parts = ["Found conflicting index store units for '\(file)' in module '\(module)'."]
+            if targets.count > 1 {
+                parts.append("The units have conflicting build targets: \(targets.sorted().joined(separator: ", ")).")
+            }
+            parts.append("If you passed the '--index-store-path' option, ensure that Xcode is not open with a project that may write to this index store while Periphery is running.")
+            return parts.joined(separator: " ")
         }
     }