diff --git a/src/backends/shared/NativeToolEngine.ts b/src/backends/shared/NativeToolEngine.ts
index 58b1ca9b..47f7c0a3 100644
--- a/src/backends/shared/NativeToolEngine.ts
+++ b/src/backends/shared/NativeToolEngine.ts
@@ -17,6 +17,8 @@
  * the subprocess pattern captured here.
  */
 
+import type { z } from 'zod';
+import { getEngineSettings } from '../../config/engineSettings.js';
 import type {
 	AgentEngine,
 	AgentEngineDefinition,
@@ -102,6 +104,28 @@ export abstract class NativeToolEngine implements AgentEngine {
 		await cleanupContextFiles(plan.repoDir);
 	}
 
+	/**
+	 * Resolve engine-specific settings from an execution plan.
+	 *
+	 * Reads from `input.engineSettings ?? input.project.engineSettings` and
+	 * validates the result against `schema`. Returns `{}` (empty object typed
+	 * as `z.infer<S>`) when no settings are configured for this engine.
+	 *
+	 * Subclasses should call this inside `execute()` with their own schema,
+	 * passing the engine id via `this.definition.id`:
+	 *
+	 * ```ts
+	 * const raw = this.resolveSettings(input, MyEngineSettingsSchema);
+	 * ```
+	 */
+	protected resolveSettings<S extends z.ZodType<Record<string, unknown>>>(
+		input: AgentExecutionPlan,
+		schema: S,
+	): z.infer<S> {
+		const effectiveSettings = input.engineSettings ?? input.project.engineSettings;
+		return getEngineSettings(effectiveSettings, this.definition.id, schema) ?? ({} as z.infer<S>);
+	}
+
 	/**
 	 * Subclasses must provide the actual subprocess execution logic.
 	 */
diff --git a/src/config/engineSettings.ts b/src/config/engineSettings.ts
index 142bd218..33ddffeb 100644
--- a/src/config/engineSettings.ts
+++ b/src/config/engineSettings.ts
@@ -1,30 +1,16 @@
 import { z } from 'zod';
 
-// Import and re-export schemas from engine directories.
-import { ClaudeCodeSettingsSchema } from '../backends/claude-code/settings.js';
-export { ClaudeCodeSettingsSchema };
-export type { ClaudeCodeSettings } from '../backends/claude-code/settings.js';
-import { CodexSettingsSchema } from '../backends/codex/settings.js';
-export { CodexSettingsSchema };
-export type { CodexSettings } from '../backends/codex/settings.js';
-import { OpenCodeSettingsSchema } from '../backends/opencode/settings.js';
-export { OpenCodeSettingsSchema };
-export type { OpenCodeSettings } from '../backends/opencode/settings.js';
-
 /**
  * Dynamic registry of engine settings schemas.
  * Engines register their schema during bootstrap via registerEngineSettingsSchema().
+ *
+ * Schemas are registered exclusively through registerBuiltInEngines() (called from
+ * bootstrap.ts) — there are no static pre-registration imports here. All entry
+ * points (router, worker, dashboard) must call registerBuiltInEngines() before any
+ * config parsing that uses EngineSettingsSchema.
  */
 const ENGINE_SETTINGS_SCHEMAS: Map<string, z.ZodType<Record<string, unknown>>> = new Map();
 
-// Pre-register built-in engine settings schemas at module initialization.
-// Any process that imports EngineSettingsSchema (via config/schema.ts) will
-// have these registered automatically — no explicit registerBuiltInEngines()
-// call required for schema validation.
-ENGINE_SETTINGS_SCHEMAS.set('claude-code', ClaudeCodeSettingsSchema);
-ENGINE_SETTINGS_SCHEMAS.set('codex', CodexSettingsSchema);
-ENGINE_SETTINGS_SCHEMAS.set('opencode', OpenCodeSettingsSchema);
-
 /**
  * Register a settings schema for an engine. Called during bootstrap when an engine
  * implementing getSettingsSchema() is registered.
diff --git a/tests/unit/backends/NativeToolEngine.test.ts b/tests/unit/backends/NativeToolEngine.test.ts
index 522ce35f..56037cf5 100644
--- a/tests/unit/backends/NativeToolEngine.test.ts
+++ b/tests/unit/backends/NativeToolEngine.test.ts
@@ -6,6 +6,7 @@
  */
 
 import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+import { z } from 'zod';
 import { NativeToolEngine } from '../../../src/backends/shared/NativeToolEngine.js';
 import type {
 	AgentEngineDefinition,
@@ -61,6 +62,14 @@ class StubEngine extends NativeToolEngine {
 		throw new Error(`Incompatible model: ${cascadeModel}`);
 	}
 
+	// Expose protected resolveSettings for testing
+	resolveSettingsPublic<S extends z.ZodType<Record<string, unknown>>>(
+		input: AgentExecutionPlan,
+		schema: S,
+	): z.infer<S> {
+		return this.resolveSettings(input, schema);
+	}
+
 	// Simple stub: always returns a successful result
 	async execute(_input: AgentExecutionPlan): Promise<AgentEngineResult> {
 		return { success: true, output: 'stub output' };
@@ -245,6 +254,73 @@ describe('NativeToolEngine (via StubEngine)', () => {
 		});
 	});
 
+	// -------------------------------------------------------------------------
+	// resolveSettings — reads engine settings from the execution plan
+	// -------------------------------------------------------------------------
+	describe('resolveSettings', () => {
+		const StubSchema = z.object({
+			timeout: z.number().optional(),
+			mode: z.string().optional(),
+		});
+
+		it('returns {} when no engineSettings or project.engineSettings are set', () => {
+			const plan = makeMinimalPlan();
+			const result = engine.resolveSettingsPublic(plan, StubSchema);
+			expect(result).toEqual({});
+		});
+
+		it('returns settings from project.engineSettings when input.engineSettings is absent', () => {
+			const plan = makeMinimalPlan({
+				project: {
+					id: 'test-project',
+					orgId: 'org-1',
+					name: 'Test',
+					repo: 'owner/repo',
+					baseBranch: 'main',
+					branchPrefix: 'feature/',
+					pm: { type: 'trello' },
+					engineSettings: { stub: { timeout: 5000, mode: 'fast' } },
+				} as AgentExecutionPlan['project'],
+			});
+			const result = engine.resolveSettingsPublic(plan, StubSchema);
+			expect(result).toEqual({ timeout: 5000, mode: 'fast' });
+		});
+
+		it('prefers input.engineSettings over project.engineSettings', () => {
+			const plan = makeMinimalPlan({
+				project: {
+					id: 'test-project',
+					orgId: 'org-1',
+					name: 'Test',
+					repo: 'owner/repo',
+					baseBranch: 'main',
+					branchPrefix: 'feature/',
+					pm: { type: 'trello' },
+					engineSettings: { stub: { timeout: 1000 } },
+				} as AgentExecutionPlan['project'],
+				engineSettings: { stub: { timeout: 9999 } },
+			});
+			const result = engine.resolveSettingsPublic(plan, StubSchema);
+			expect(result).toEqual({ timeout: 9999 });
+		});
+
+		it('returns {} when engineSettings exists but has no entry for this engine id', () => {
+			const plan = makeMinimalPlan({
+				engineSettings: { 'other-engine': { timeout: 5000 } },
+			});
+			const result = engine.resolveSettingsPublic(plan, StubSchema);
+			expect(result).toEqual({});
+		});
+
+		it('uses definition.id ("stub") as the engine settings key', () => {
+			const plan = makeMinimalPlan({
+				engineSettings: { stub: { timeout: 42 } },
+			});
+			const result = engine.resolveSettingsPublic(plan, StubSchema);
+			expect(result.timeout).toBe(42);
+		});
+	});
+
 	// -------------------------------------------------------------------------
 	// implements AgentEngine interface
 	// -------------------------------------------------------------------------