diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index df942a32b0..52eb03a432 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -318,6 +318,33 @@ jobs:
       - name: Validate install manifest
         run: npm run validate:manifest
 
+  registry-determinism:
+    name: Entity Registry Determinism
+    needs: changes
+    if: ${{ needs.changes.outputs.code == 'true' }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v6
+        with:
+          node-version: '20'
+          cache: 'npm'
+          cache-dependency-path: package-lock.json
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Validate registry determinism
+        # Re-runs populate-entity-registry.js and compares output against the
+        # committed entity-registry.yaml. Catches the category of drift that
+        # produced #754 (regen against partially-edited working tree). See #758.
+        run: npm run validate:registry-determinism
+
   ide-sync-validation:
     name: IDE Command Sync Validation
     needs: changes
@@ -409,6 +436,7 @@ jobs:
         test,
         story-validation,
         manifest-validation,
+        registry-determinism,
         ide-sync-validation,
         installer-smoke-test,
         compatibility-parity-gate,
@@ -435,6 +463,7 @@ jobs:
           echo "  Tests: ${{ needs.test.result }}"
           echo "  Story Validation: ${{ needs.story-validation.result }}"
           echo "  Manifest Validation: ${{ needs.manifest-validation.result }}"
+          echo "  Registry Determinism: ${{ needs.registry-determinism.result }}"
           echo "  IDE Sync Validation: ${{ needs.ide-sync-validation.result }}"
           echo "  Installer Smoke Test: ${{ needs.installer-smoke-test.result }}"
           echo "  Dependency Validation: ${{ needs.dependency-validation.result }}"
@@ -480,6 +509,12 @@ jobs:
             FAILED=true
           fi
 
+          # Registry Determinism: fail if ran and didn't succeed
+          if [ "${{ needs.registry-determinism.result }}" == "failure" ]; then
+            echo "❌ Entity registry determinism check failed — regen drift detected"
+            FAILED=true
+          fi
+
           # IDE Sync: fail if ran and didn't succeed
           if [ "${{ needs.ide-sync-validation.result }}" == "failure" ]; then
             echo "❌ IDE sync validation failed"
diff --git a/package.json b/package.json
index 296abf2e7c..cad37a69bb 100644
--- a/package.json
+++ b/package.json
@@ -71,6 +71,7 @@
     "release:test": "semantic-release --dry-run --no-ci || echo 'Config test complete - authentication errors are expected locally'",
     "generate:manifest": "node scripts/generate-install-manifest.js",
     "validate:manifest": "node scripts/validate-manifest.js",
+    "validate:registry-determinism": "node scripts/validate-registry-determinism.js",
     "validate:structure": "node .aiox-core/infrastructure/scripts/source-tree-guardian/index.js",
     "validate:agents": "node .aiox-core/infrastructure/scripts/validate-agents.js",
     "sync:ide": "node .aiox-core/infrastructure/scripts/ide-sync/index.js sync",
diff --git a/scripts/validate-registry-determinism.js b/scripts/validate-registry-determinism.js
new file mode 100644
index 0000000000..8bd64bb6a6
--- /dev/null
+++ b/scripts/validate-registry-determinism.js
@@ -0,0 +1,173 @@
+#!/usr/bin/env node
+/**
+ * Validate Entity Registry Determinism
+ *
+ * Re-runs the IDS registry populator against the current source tree and
+ * compares the output against the committed `.aiox-core/data/entity-registry.yaml`.
+ * Mutations of `dependencies` and `usedBy` arrays — not just timestamp drift —
+ * fail the check. Catches the category of drift that produced #754 (false
+ * alarm): a partially-edited working tree silently producing a registry that
+ * doesn't match what the algorithm would produce on the same source.
+ *
+ * @script scripts/validate-registry-determinism.js
+ * @issue #758
+ *
+ * Usage:
+ *   node scripts/validate-registry-determinism.js
+ *   npm run validate:registry-determinism
+ *
+ * Exit codes:
+ *   0 - Committed registry matches a clean regen
+ *   1 - Drift detected — run populate-entity-registry.js locally and commit
+ */
+
+'use strict';
+
+const fs = require('fs');
+const path = require('path');
+const yaml = require('js-yaml');
+const { execFileSync } = require('child_process');
+
+const REPO_ROOT = path.resolve(__dirname, '..');
+const REGISTRY_PATH = path.join(REPO_ROOT, '.aiox-core', 'data', 'entity-registry.yaml');
+const POPULATOR_PATH = path.join(REPO_ROOT, '.aiox-core', 'development', 'scripts', 'populate-entity-registry.js');
+
+// Fields that legitimately differ between runs (clock-driven or
+// content-hash-driven and re-computed on every regen). We compare structure
+// minus these.
+const VOLATILE_FIELDS = new Set(['lastUpdated', 'lastVerified', 'checksum']);
+
+/**
+ * Recursively strip volatile fields from a parsed YAML structure.
+ */
+function stripVolatile(node) {
+  if (Array.isArray(node)) {
+    return node.map(stripVolatile);
+  }
+  if (node && typeof node === 'object') {
+    const out = {};
+    for (const key of Object.keys(node)) {
+      if (VOLATILE_FIELDS.has(key)) continue;
+      out[key] = stripVolatile(node[key]);
+    }
+    return out;
+  }
+  return node;
+}
+
+function fail(message, details) {
+  console.error('\n❌ Registry determinism check FAILED');
+  console.error('   ' + message);
+  if (details) {
+    console.error('');
+    console.error(details);
+  }
+  console.error('');
+  console.error('   Remediate locally:');
+  console.error('     node .aiox-core/development/scripts/populate-entity-registry.js');
+  console.error('     git add .aiox-core/data/entity-registry.yaml');
+  console.error('     git commit -m "chore(ids): regen entity-registry"');
+  console.error('');
+  process.exit(1);
+}
+
+function main() {
+  if (!fs.existsSync(REGISTRY_PATH)) {
+    fail(`Registry not found at ${REGISTRY_PATH}`);
+  }
+  if (!fs.existsSync(POPULATOR_PATH)) {
+    fail(`Populator script not found at ${POPULATOR_PATH}`);
+  }
+
+  // 1. Snapshot the committed registry so we can restore it regardless of outcome.
+  const committedYaml = fs.readFileSync(REGISTRY_PATH, 'utf8');
+  const committedParsed = yaml.load(committedYaml);
+
+  let regennedYaml;
+  let regennedParsed;
+  try {
+    // 2. Run the populator. It mutates `REGISTRY_PATH` in place.
+    execFileSync('node', [POPULATOR_PATH], {
+      cwd: REPO_ROOT,
+      stdio: 'pipe',
+    });
+    regennedYaml = fs.readFileSync(REGISTRY_PATH, 'utf8');
+    regennedParsed = yaml.load(regennedYaml);
+  } finally {
+    // 3. Restore the committed registry no matter what — the populator
+    //    mutated the working tree and CI/local should not carry that drift
+    //    forward in subsequent steps. Tests + lint may also rely on the
+    //    committed state.
+    fs.writeFileSync(REGISTRY_PATH, committedYaml);
+  }
+
+  // 4. Compare structures with volatile fields stripped.
+  const committedStripped = stripVolatile(committedParsed);
+  const regennedStripped = stripVolatile(regennedParsed);
+
+  // Sort keys recursively before stringifying so map ordering doesn't trigger
+  // false positives. (JSON.stringify's second arg is a replacer, not a key
+  // sorter — passing an array there would FILTER keys instead.)
+  const sortedStringify = (value) =>
+    JSON.stringify(value, (_key, v) => {
+      if (v && typeof v === 'object' && !Array.isArray(v)) {
+        const sorted = {};
+        for (const k of Object.keys(v).sort()) {
+          sorted[k] = v[k];
+        }
+        return sorted;
+      }
+      return v;
+    });
+
+  const committedJson = sortedStringify(committedStripped);
+  const regennedJson = sortedStringify(regennedStripped);
+
+  if (committedJson === regennedJson) {
+    console.log('✅ Registry determinism check PASSED');
+    console.log(`   ${committedParsed.metadata.entityCount} entities, structure matches regen output.`);
+    return;
+  }
+
+  // 5. Diff failed — emit an actionable summary of what drifted.
+  const drifts = [];
+  const committedEntities = committedStripped.entities || {};
+  const regennedEntities = regennedStripped.entities || {};
+
+  const allCategories = new Set([
+    ...Object.keys(committedEntities),
+    ...Object.keys(regennedEntities),
+  ]);
+
+  for (const category of allCategories) {
+    const committedCat = committedEntities[category] || {};
+    const regennedCat = regennedEntities[category] || {};
+    const allNames = new Set([...Object.keys(committedCat), ...Object.keys(regennedCat)]);
+    for (const name of allNames) {
+      const c = committedCat[name];
+      const r = regennedCat[name];
+      if (!c || !r) {
+        drifts.push(`  [${category}] ${name}: ${!c ? 'added by regen' : 'removed by regen'}`);
+        continue;
+      }
+      const cDeps = JSON.stringify((c.dependencies || []).slice().sort());
+      const rDeps = JSON.stringify((r.dependencies || []).slice().sort());
+      if (cDeps !== rDeps) {
+        drifts.push(`  [${category}] ${name}: dependencies differ`);
+      }
+      const cUsed = JSON.stringify((c.usedBy || []).slice().sort());
+      const rUsed = JSON.stringify((r.usedBy || []).slice().sort());
+      if (cUsed !== rUsed) {
+        drifts.push(`  [${category}] ${name}: usedBy differs`);
+      }
+    }
+  }
+
+  const detail = drifts.length
+    ? drifts.slice(0, 30).join('\n') + (drifts.length > 30 ? `\n  ... and ${drifts.length - 30} more` : '')
+    : `(structural delta beyond dependency/usedBy — diff committed vs regenned ${REGISTRY_PATH})`;
+
+  fail(`${drifts.length} entries diverged between committed registry and clean regen output.`, detail);
+}
+
+main();