diff --git a/.changeset/751-config-prototype-pollution-codeql-alert-26.md b/.changeset/751-config-prototype-pollution-codeql-alert-26.md
new file mode 100644
index 000000000..2e638c05e
--- /dev/null
+++ b/.changeset/751-config-prototype-pollution-codeql-alert-26.md
@@ -0,0 +1,5 @@
+---
+type: Security
+pr: 752
+---
+**`gsd-tools config-set` prototype-pollution guard hardened and regression-tested.** The guard that blocks `__proto__`, `prototype`, and `constructor` segments in dotted config keys now uses inline literal comparisons at each property-write site (instead of a pre-loop `Set` check), so CodeQL's `js/prototype-pollution-utility` analysis recognises it as a sanitising barrier and code-scanning alert #26 clears. Runtime behaviour is unchanged from #663. Added regression tests that drive schema-valid dynamic-prefix keys (`agent_skills.__proto__`, `agent_skills.constructor`, `features.__proto__`, `review.models.constructor`) all the way to the guard — these reach `setConfigValue` past the schema gate and were previously the guard's only untested attack surface. (#751)
diff --git a/src/config.cts b/src/config.cts
index a0eb45f7c..4fa4d9efc 100644
--- a/src/config.cts
+++ b/src/config.cts
@@ -429,22 +429,31 @@ function setConfigValue(cwd: string, keyPath: string, parsedValue: unknown): Set
       error('Failed to read config.json: ' + (err as Error).message, ERROR_REASON.CONFIG_PARSE_FAILED);
     }
 
-    // Set nested value using dot notation (e.g., "workflow.research")
+    // Set nested value using dot notation (e.g., "workflow.research").
+    // Prototype-pollution guard: reject dangerous segments via inline literal
+    // comparisons on the exact key used to index `current`, immediately before
+    // each write. The inline comparison is the barrier CodeQL's
+    // js/prototype-pollution-utility query recognises — the previous Set-based
+    // pre-loop check was functionally correct but not traced through, so
+    // code-scanning alert #26 kept firing. Behaviour is unchanged from #663.
     const keys = keyPath.split('.');
-    const FORBIDDEN_KEYS = new Set(['__proto__', 'prototype', 'constructor']);
-    if (keys.some((k) => FORBIDDEN_KEYS.has(k))) {
-      error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
-    }
     let current: Record<string, unknown> = config;
     for (let i = 0; i < keys.length - 1; i++) {
       const key = keys[i];
+      if (key === '__proto__' || key === 'prototype' || key === 'constructor') {
+        error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
+      }
       if (current[key] === undefined || typeof current[key] !== 'object') {
         current[key] = {};
       }
       current = current[key] as Record<string, unknown>;
     }
-    const previousValue = current[keys[keys.length - 1]]; // Capture previous value before overwriting
-    current[keys[keys.length - 1]] = parsedValue;
+    const lastKey = keys[keys.length - 1];
+    if (lastKey === '__proto__' || lastKey === 'prototype' || lastKey === 'constructor') {
+      error('Invalid config key (prototype pollution guard): ' + keyPath, ERROR_REASON.CONFIG_PARSE_FAILED);
+    }
+    const previousValue = current[lastKey]; // Capture previous value before overwriting
+    current[lastKey] = parsedValue;
 
     // Write back
     try {
diff --git a/tests/config.test.cjs b/tests/config.test.cjs
index d369d29fe..1180f5222 100644
--- a/tests/config.test.cjs
+++ b/tests/config.test.cjs
@@ -1158,6 +1158,127 @@ describe('config-set prototype-pollution guard (#663)', () => {
   });
 });
 
+// ─── config-set prototype-pollution guard via dynamic-key prefixes (alert #26) ─
+
+describe('config-set prototype-pollution guard via dynamic-key prefixes (alert #26)', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempProject();
+    // Initialise config so there is a config.json to write to.
+    runGsdTools('config-ensure-section', tmpDir);
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('agent_skills.__proto__ is blocked by setConfigValue guard (not schema gate)', () => {
+    const result = runGsdTools('config-set agent_skills.__proto__ somevalue', tmpDir);
+
+    assert.strictEqual(result.success, false, `Expected failure but got: ${result.output}`);
+
+    // Must be the pollution guard, not the schema gate.
+    assert.ok(
+      result.error.includes('prototype pollution guard'),
+      `Expected "prototype pollution guard" in error, got: ${result.error}`,
+    );
+    // No schema-gate message.
+    assert.ok(
+      !result.error.includes('Unknown config key'),
+      `Should not hit schema gate, got: ${result.error}`,
+    );
+
+    // No prototype pollution occurred.
+    assert.strictEqual(({}).somevalue, undefined, 'agent_skills.__proto__: {}.somevalue should be undefined');
+    assert.strictEqual(Object.prototype.hasOwnProperty.call(Object.prototype, 'somevalue'), false,
+      'agent_skills.__proto__: Object.prototype should not gain "somevalue"');
+  });
+
+  test('agent_skills.constructor is blocked by setConfigValue guard (not schema gate)', () => {
+    const result = runGsdTools('config-set agent_skills.constructor somevalue', tmpDir);
+
+    assert.strictEqual(result.success, false, `Expected failure but got: ${result.output}`);
+
+    assert.ok(
+      result.error.includes('prototype pollution guard'),
+      `Expected "prototype pollution guard" in error, got: ${result.error}`,
+    );
+    assert.ok(
+      !result.error.includes('Unknown config key'),
+      `Should not hit schema gate, got: ${result.error}`,
+    );
+
+    assert.strictEqual(Object.prototype.hasOwnProperty.call(Object.prototype, 'somevalue'), false,
+      'agent_skills.constructor: Object.prototype should not gain "somevalue"');
+  });
+
+  test('agent_skills.prototype is blocked by setConfigValue guard (not schema gate)', () => {
+    const result = runGsdTools('config-set agent_skills.prototype somevalue', tmpDir);
+
+    assert.strictEqual(result.success, false, `Expected failure but got: ${result.output}`);
+
+    assert.ok(
+      result.error.includes('prototype pollution guard'),
+      `Expected "prototype pollution guard" in error, got: ${result.error}`,
+    );
+    assert.ok(
+      !result.error.includes('Unknown config key'),
+      `Should not hit schema gate, got: ${result.error}`,
+    );
+
+    assert.strictEqual(Object.prototype.hasOwnProperty.call(Object.prototype, 'somevalue'), false,
+      'agent_skills.prototype: Object.prototype should not gain "somevalue"');
+  });
+
+  test('features.__proto__ is blocked by setConfigValue guard (not schema gate)', () => {
+    const result = runGsdTools('config-set features.__proto__ somevalue', tmpDir);
+
+    assert.strictEqual(result.success, false, `Expected failure but got: ${result.output}`);
+
+    assert.ok(
+      result.error.includes('prototype pollution guard'),
+      `Expected "prototype pollution guard" in error, got: ${result.error}`,
+    );
+    assert.ok(
+      !result.error.includes('Unknown config key'),
+      `Should not hit schema gate, got: ${result.error}`,
+    );
+
+    assert.strictEqual(({}).somevalue, undefined, 'features.__proto__: {}.somevalue should be undefined');
+    assert.strictEqual(Object.prototype.hasOwnProperty.call(Object.prototype, 'somevalue'), false,
+      'features.__proto__: Object.prototype should not gain "somevalue"');
+  });
+
+  test('review.models.constructor is blocked by setConfigValue guard (not schema gate)', () => {
+    const result = runGsdTools('config-set review.models.constructor somevalue', tmpDir);
+
+    assert.strictEqual(result.success, false, `Expected failure but got: ${result.output}`);
+
+    assert.ok(
+      result.error.includes('prototype pollution guard'),
+      `Expected "prototype pollution guard" in error, got: ${result.error}`,
+    );
+    assert.ok(
+      !result.error.includes('Unknown config key'),
+      `Should not hit schema gate, got: ${result.error}`,
+    );
+
+    assert.strictEqual(Object.prototype.hasOwnProperty.call(Object.prototype, 'somevalue'), false,
+      'review.models.constructor: Object.prototype should not gain "somevalue"');
+  });
+
+  test('positive control: agent_skills.sonnet-coder with valid value succeeds', () => {
+    const result = runGsdTools('config-set agent_skills.sonnet-coder true', tmpDir);
+
+    assert.ok(result.success, `Legitimate agent_skills key rejected unexpectedly: ${result.error}`);
+
+    const config = readConfig(tmpDir);
+    assert.strictEqual(config.agent_skills['sonnet-coder'], true,
+      'agent_skills.sonnet-coder should be written to config.json');
+  });
+});
+
 // ─── plan_review.source_grounding + _authority (#22) ─────────────────────────
 
 describe('plan_review.source_grounding and plan_review.source_grounding_authority (#22)', () => {