diff --git a/internal/command/generate.go b/internal/command/generate.go
index dff6012..2603cd4 100644
--- a/internal/command/generate.go
+++ b/internal/command/generate.go
@@ -196,6 +196,14 @@ manifests. All resources and links between Workloads will be resolved and provis
 					if p, ok := internal.FindFirstUnresolvedSecretRef("", manifest); ok {
 						return errors.Errorf("unresolved secret ref in manifest: %s", p)
 					}
+					mSig := buildManifestSignature(manifest)
+					outputManifests = slices.DeleteFunc(outputManifests, func(other map[string]interface{}) bool {
+						if buildManifestSignature(other) == mSig {
+							slog.Info(fmt.Sprintf("Overriding duplicate resource manifest %s", mSig))
+							return true
+						}
+						return false
+					})
 					outputManifests = append(outputManifests, manifest)
 				}
 				slog.Info(fmt.Sprintf("Wrote %d resource manifests to manifests buffer for resource '%s'", len(res.Extras.Manifests), id))
@@ -217,6 +225,14 @@ manifests. All resources and links between Workloads will be resolved and provis
 				if p, ok := internal.FindFirstUnresolvedSecretRef("", intermediate); ok {
 					return errors.Errorf("unresolved secret ref in manifest: %s", p)
 				}
+				mSig := buildManifestSignature(intermediate)
+				outputManifests = slices.DeleteFunc(outputManifests, func(other map[string]interface{}) bool {
+					if buildManifestSignature(other) == mSig {
+						slog.Info(fmt.Sprintf("Overriding duplicate resource manifest %s", mSig))
+						return true
+					}
+					return false
+				})
 				outputManifests = append(outputManifests, intermediate)
 			}
 			slog.Info(fmt.Sprintf("Wrote %d manifests to manifests buffer for workload '%s'", len(manifests), workloadName))
@@ -335,6 +351,17 @@ func parseAndApplyManifestPatches(entry string, flagName string, manifests []map
 	return outManifests, nil
 }
 
+// buildManifestSignature builds a unique manifest signature for each manifest coming out of a resource. This is used
+// to deduplicate resource manifests when they share state.
+func buildManifestSignature(n map[string]interface{}) string {
+	apiVersion, _ := n["apiVersion"].(string)
+	kind, _ := n["kind"].(string)
+	metadata, _ := n["metadata"].(map[string]interface{})
+	namespace, _ := metadata["namespace"].(string)
+	name, _ := metadata["name"].(string)
+	return fmt.Sprintf("%s/%s/%s/%s", apiVersion, kind, namespace, name)
+}
+
 func init() {
 	generateCmd.Flags().StringP(generateCmdOutputFlag, "o", "manifests.yaml", "The output manifests file to write the manifests to")
 	generateCmd.Flags().String(generateCmdOverridesFileFlag, "", "An optional file of Score overrides to merge in")
diff --git a/internal/command/generate_test.go b/internal/command/generate_test.go
index 76150e1..f1d7fa4 100644
--- a/internal/command/generate_test.go
+++ b/internal/command/generate_test.go
@@ -18,6 +18,7 @@ import (
 	"context"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -236,3 +237,39 @@ containers:
 	assert.EqualError(t, err, "cannot use --override-property, --overrides-file, or --image when 0 or more than 1 score files are provided")
 	assert.Equal(t, "", stdout)
 }
+
+func TestDeduplicateResourceManifests(t *testing.T) {
+	td := changeToTempDir(t)
+	assert.NoError(t, os.WriteFile(filepath.Join(td, "score.yaml"), []byte(`
+apiVersion: score.dev/v1b1
+metadata:
+  name: example-a
+containers:
+  hello:
+    image: foo
+resources:
+  d1:
+    type: dummy
+  d2:
+    type: dummy
+`), 0644))
+	_, _, err := executeAndResetCommand(context.Background(), rootCmd, []string{"init"})
+	require.NoError(t, err)
+	assert.NoError(t, os.WriteFile(filepath.Join(td, ".score-k8s", "00.provisioners.yaml"), []byte(`
+- uri: template://dummy
+  type: dummy
+  manifests: |
+    - apiVersion: v1
+      kind: Secret
+      metadata:
+        name: my-secret
+      data:
+        fruit: {{ b64enc "banana" }}
+`), 0644))
+	_, stderr, err := executeAndResetCommand(context.Background(), rootCmd, []string{"generate", "score.yaml"})
+	t.Log(string(stderr))
+	require.NoError(t, err)
+	rawManifests, err := os.ReadFile(filepath.Join(td, "manifests.yaml"))
+	require.NoError(t, err)
+	assert.Equal(t, strings.Count(string(rawManifests), "kind: Secret"), 1, "failed to find in", string(rawManifests))
+}