diff --git a/graphql/env/__tests__/__snapshots__/merge.test.ts.snap b/graphql/env/__tests__/__snapshots__/merge.test.ts.snap
index 02c79c085..636127402 100644
--- a/graphql/env/__tests__/__snapshots__/merge.test.ts.snap
+++ b/graphql/env/__tests__/__snapshots__/merge.test.ts.snap
@@ -12,10 +12,6 @@ exports[`getEnvOptions merges pgpm defaults, graphql defaults, config, env, and
     ],
     "isPublic": true,
     "metaSchemas": [
-      "config_meta",
-      "services_public",
-      "metaschema_public",
-      "metaschema_modules_public",
       "env_meta1",
       "env_meta2",
     ],
@@ -75,9 +71,6 @@ exports[`getEnvOptions merges pgpm defaults, graphql defaults, config, env, and
     "graphileBuildOptions": {},
     "overrideSettings": {},
     "schema": [
-      "config_schema",
-      "env_schema_a",
-      "env_schema_b",
       "override_schema",
     ],
   },
diff --git a/graphql/env/__tests__/merge.test.ts b/graphql/env/__tests__/merge.test.ts
index 4cc6e240f..edbc3f6df 100644
--- a/graphql/env/__tests__/merge.test.ts
+++ b/graphql/env/__tests__/merge.test.ts
@@ -84,8 +84,8 @@ describe('getEnvOptions', () => {
     expect(result).toMatchSnapshot();
   });
 
-  it('dedupes graphql array fields across config, env, and overrides', () => {
-    tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'graphql-env-dedupe-'));
+  it('replaces graphql array fields with later values (overrides win)', () => {
+    tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'graphql-env-replace-'));
     writeConfig(tempDir, {
       graphile: {
         schema: ['config_schema', 'shared_schema']
@@ -116,25 +116,9 @@ describe('getEnvOptions', () => {
       testEnv
     );
 
-    expect(result.graphile?.schema).toEqual([
-      'config_schema',
-      'shared_schema',
-      'env_schema',
-      'override_schema'
-    ]);
-    expect(result.api?.exposedSchemas).toEqual([
-      'public',
-      'shared',
-      'env_schema',
-      'override_schema'
-    ]);
-    expect(result.api?.metaSchemas).toEqual([
-      'metaschema_public',
-      'services_public',
-      'config_meta',
-      'metaschema_modules_public',
-      'env_meta',
-      'override_meta'
-    ]);
+    // Arrays are replaced, not merged - overrides win completely
+    expect(result.graphile?.schema).toEqual(['override_schema', 'shared_schema']);
+    expect(result.api?.exposedSchemas).toEqual(['public', 'override_schema']);
+    expect(result.api?.metaSchemas).toEqual(['env_meta', 'override_meta']);
   });
 });
diff --git a/graphql/env/src/merge.ts b/graphql/env/src/merge.ts
index c9e1e235a..669c75269 100644
--- a/graphql/env/src/merge.ts
+++ b/graphql/env/src/merge.ts
@@ -1,6 +1,6 @@
 import deepmerge from 'deepmerge';
 import { ConstructiveOptions, constructiveGraphqlDefaults } from '@constructive-io/graphql-types';
-import { getEnvOptions as getPgpmEnvOptions, loadConfigSync, mergeArraysUnique } from '@pgpmjs/env';
+import { getEnvOptions as getPgpmEnvOptions, loadConfigSync, replaceArrays } from '@pgpmjs/env';
 import { getGraphQLEnvVars } from './env';
 
 /**
@@ -47,7 +47,7 @@ export const getEnvOptions = (
     graphqlEnvOptions,
     overrides
   ], {
-    arrayMerge: mergeArraysUnique
+    arrayMerge: replaceArrays
   }) as ConstructiveOptions;
 };
 
diff --git a/pgpm/env/__tests__/merge.test.ts b/pgpm/env/__tests__/merge.test.ts
index f6db3d26e..c880841c5 100644
--- a/pgpm/env/__tests__/merge.test.ts
+++ b/pgpm/env/__tests__/merge.test.ts
@@ -180,8 +180,8 @@ describe('getEnvOptions', () => {
     expect(result).toMatchSnapshot();
   });
 
-  it('dedupes array fields across config, env, and overrides', () => {
-    tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'pgpm-env-dedupe-'));
+  it('replaces array fields with later values (overrides win)', () => {
+    tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'pgpm-env-replace-'));
     writeConfig(tempDir, {
       db: {
         extensions: ['uuid', 'postgis']
@@ -219,25 +219,10 @@ describe('getEnvOptions', () => {
 
     const result = getEnvOptions(overrides, tempDir, testEnv) as PgpmOptionsWithPackages;
 
-    expect(result.db?.extensions).toEqual([
-      'uuid',
-      'postgis',
-      'pgcrypto',
-      'hstore'
-    ]);
-    expect(result.jobs?.worker?.supported).toEqual([
-      'alpha',
-      'beta',
-      'gamma',
-      'delta',
-      'epsilon'
-    ]);
-    expect(result.jobs?.scheduler?.supported).toEqual([
-      'beta',
-      'gamma',
-      'delta',
-      'zeta'
-    ]);
-    expect(result.packages).toEqual(['testing/*', 'packages/*', 'extensions/*']);
+    // Arrays are replaced, not merged - overrides win completely
+    expect(result.db?.extensions).toEqual(['uuid', 'hstore']);
+    expect(result.jobs?.worker?.supported).toEqual(['delta', 'epsilon']);
+    expect(result.jobs?.scheduler?.supported).toEqual(['gamma', 'zeta']);
+    expect(result.packages).toEqual(['testing/*', 'extensions/*']);
   });
 });
diff --git a/pgpm/env/src/index.ts b/pgpm/env/src/index.ts
index 66fb144f2..9ec47ea63 100644
--- a/pgpm/env/src/index.ts
+++ b/pgpm/env/src/index.ts
@@ -11,6 +11,6 @@ export {
 } from './config';
 export type { WorkspaceType } from './config';
 export { getEnvVars, getNodeEnv, parseEnvBoolean, parseEnvNumber } from './env';
-export { walkUp, mergeArraysUnique } from './utils';
+export { walkUp, replaceArrays } from './utils';
 
 export type { PgpmOptions, PgTestConnectionOptions, DeploymentOptions } from '@pgpmjs/types';
diff --git a/pgpm/env/src/merge.ts b/pgpm/env/src/merge.ts
index 1e0a08074..d0e920db3 100644
--- a/pgpm/env/src/merge.ts
+++ b/pgpm/env/src/merge.ts
@@ -2,7 +2,7 @@ import deepmerge from 'deepmerge';
 import { pgpmDefaults, PgpmOptions, PgTestConnectionOptions, DeploymentOptions } from '@pgpmjs/types';
 import { loadConfigSync } from './config';
 import { getEnvVars } from './env';
-import { mergeArraysUnique } from './utils';
+import { replaceArrays } from './utils';
 
 /**
  * Get core PGPM environment options by merging:
@@ -26,7 +26,7 @@ export const getEnvOptions = (
   const envOptions = getEnvVars(env);
   
   return deepmerge.all([pgpmDefaults, configOptions, envOptions, overrides], {
-    arrayMerge: mergeArraysUnique
+    arrayMerge: replaceArrays
   });
 };
 
diff --git a/pgpm/env/src/utils.ts b/pgpm/env/src/utils.ts
index 083be7831..2b8cba957 100644
--- a/pgpm/env/src/utils.ts
+++ b/pgpm/env/src/utils.ts
@@ -26,11 +26,14 @@ export const walkUp = (startDir: string, filename: string): string => {
   throw new Error(`File "${filename}" not found in any parent directories.`);
 };
 
-export const mergeArraysUnique = <T>(
-  target: T[],
+/**
+ * Array merge strategy that replaces target array with source array.
+ * This allows later configuration sources to completely override earlier ones.
+ */
+export const replaceArrays = <T>(
+  _target: T[],
   source: T[],
   _options?: unknown
 ): T[] => {
-  const merged = [...target, ...source];
-  return [...new Set(merged)];
+  return source;
 };