diff --git a/.changeset/tame-parents-drive.md b/.changeset/tame-parents-drive.md
new file mode 100644
index 00000000000..cdc37de4137
--- /dev/null
+++ b/.changeset/tame-parents-drive.md
@@ -0,0 +1,5 @@
+---
+'@clerk/astro': major
+---
+
+Changed environment variable resolution order in `getContextEnvVar()` to prefer `process.env` over `import.meta.env`. Runtime environment variables (e.g., set in the Node.js adapter) now take precedence over build-time values statically replaced by Vite. This ensures that environment variables set at runtime behave as expected when deploying with the Astro Node adapter or similar runtime environments.
diff --git a/packages/astro/src/server/__tests__/get-safe-env.test.ts b/packages/astro/src/server/__tests__/get-safe-env.test.ts
new file mode 100644
index 00000000000..ff7e0301d6d
--- /dev/null
+++ b/packages/astro/src/server/__tests__/get-safe-env.test.ts
@@ -0,0 +1,121 @@
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+
+import { getClientSafeEnv, getSafeEnv } from '../get-safe-env';
+
+function createLocals(overrides: Partial<App.Locals> = {}): App.Locals {
+  return {
+    runtime: { env: {} as InternalEnv },
+    ...overrides,
+  } as unknown as App.Locals;
+}
+
+describe('getSafeEnv', () => {
+  beforeEach(() => {
+    vi.stubEnv('PUBLIC_CLERK_PUBLISHABLE_KEY', '');
+    vi.stubEnv('CLERK_SECRET_KEY', '');
+  });
+
+  afterEach(() => {
+    vi.unstubAllEnvs();
+  });
+
+  it('reads from locals.runtime.env first (Cloudflare)', () => {
+    const locals = createLocals({
+      runtime: {
+        env: {
+          PUBLIC_CLERK_PUBLISHABLE_KEY: 'pk_from_runtime',
+          CLERK_SECRET_KEY: 'sk_from_runtime',
+        } as InternalEnv,
+      },
+    });
+
+    // Also set process.env to verify runtime.env takes priority
+    process.env.PUBLIC_CLERK_PUBLISHABLE_KEY = 'pk_from_process';
+    process.env.CLERK_SECRET_KEY = 'sk_from_process';
+
+    const env = getSafeEnv(locals);
+
+    expect(env.pk).toBe('pk_from_runtime');
+    expect(env.sk).toBe('sk_from_runtime');
+
+    delete process.env.PUBLIC_CLERK_PUBLISHABLE_KEY;
+    delete process.env.CLERK_SECRET_KEY;
+  });
+
+  it('reads from process.env when runtime.env is not available', () => {
+    process.env.PUBLIC_CLERK_PUBLISHABLE_KEY = 'pk_from_process';
+    process.env.CLERK_SECRET_KEY = 'sk_from_process';
+
+    const locals = createLocals({ runtime: { env: undefined as unknown as InternalEnv } });
+    const env = getSafeEnv(locals);
+
+    expect(env.pk).toBe('pk_from_process');
+    expect(env.sk).toBe('sk_from_process');
+
+    delete process.env.PUBLIC_CLERK_PUBLISHABLE_KEY;
+    delete process.env.CLERK_SECRET_KEY;
+  });
+
+  it('returns undefined when no env source has the value', () => {
+    delete process.env.PUBLIC_CLERK_PUBLISHABLE_KEY;
+    delete process.env.CLERK_SECRET_KEY;
+
+    const locals = createLocals({ runtime: { env: undefined as unknown as InternalEnv } });
+    const env = getSafeEnv(locals);
+
+    expect(env.pk).toBeUndefined();
+    expect(env.sk).toBeUndefined();
+  });
+
+  it('prefers keylessPublishableKey over all env sources', () => {
+    process.env.PUBLIC_CLERK_PUBLISHABLE_KEY = 'pk_from_process';
+
+    const locals = createLocals({
+      runtime: { env: undefined as unknown as InternalEnv },
+      keylessPublishableKey: 'pk_keyless',
+    });
+    const env = getSafeEnv(locals);
+
+    expect(env.pk).toBe('pk_keyless');
+
+    delete process.env.PUBLIC_CLERK_PUBLISHABLE_KEY;
+  });
+});
+
+describe('getClientSafeEnv', () => {
+  beforeEach(() => {
+    vi.stubEnv('PUBLIC_CLERK_PUBLISHABLE_KEY', '');
+  });
+
+  afterEach(() => {
+    vi.unstubAllEnvs();
+  });
+
+  it('reads from process.env for publishableKey', () => {
+    process.env.PUBLIC_CLERK_PUBLISHABLE_KEY = 'pk_from_process';
+
+    const locals = createLocals({ runtime: { env: undefined as unknown as InternalEnv } });
+    const env = getClientSafeEnv(locals);
+
+    expect(env.publishableKey).toBe('pk_from_process');
+
+    delete process.env.PUBLIC_CLERK_PUBLISHABLE_KEY;
+  });
+
+  it('reads from process.env for all public env vars', () => {
+    process.env.PUBLIC_CLERK_DOMAIN = 'test.domain.com';
+    process.env.PUBLIC_CLERK_SIGN_IN_URL = '/sign-in';
+    process.env.PUBLIC_CLERK_SIGN_UP_URL = '/sign-up';
+
+    const locals = createLocals({ runtime: { env: undefined as unknown as InternalEnv } });
+    const env = getClientSafeEnv(locals);
+
+    expect(env.domain).toBe('test.domain.com');
+    expect(env.signInUrl).toBe('/sign-in');
+    expect(env.signUpUrl).toBe('/sign-up');
+
+    delete process.env.PUBLIC_CLERK_DOMAIN;
+    delete process.env.PUBLIC_CLERK_SIGN_IN_URL;
+    delete process.env.PUBLIC_CLERK_SIGN_UP_URL;
+  });
+});
diff --git a/packages/astro/src/server/get-safe-env.ts b/packages/astro/src/server/get-safe-env.ts
index 76600aac7c0..573ddabd053 100644
--- a/packages/astro/src/server/get-safe-env.ts
+++ b/packages/astro/src/server/get-safe-env.ts
@@ -14,7 +14,14 @@ function getContextEnvVar(envVarName: keyof InternalEnv, contextOrLocals: Contex
     return locals.runtime.env[envVarName];
   }
 
-  return import.meta.env[envVarName];
+  // Prefer process.env for runtime environments (e.g., Node.js adapter)
+  // where import.meta.env.PUBLIC_* is statically replaced at build time by Vite.
+  // Runtime values should take precedence over build-time values.
+  if (typeof process !== 'undefined' && process.env?.[envVarName]) {
+    return process.env[envVarName];
+  }
+
+  return import.meta.env[envVarName] || undefined;
 }
 
 /**
diff --git a/packages/upgrade/src/versions/core-3/changes/astro-env-var-precedence.md b/packages/upgrade/src/versions/core-3/changes/astro-env-var-precedence.md
new file mode 100644
index 00000000000..6b2551c36e1
--- /dev/null
+++ b/packages/upgrade/src/versions/core-3/changes/astro-env-var-precedence.md
@@ -0,0 +1,22 @@
+---
+title: 'Runtime environment variables now take precedence over build-time values'
+packages: ['astro']
+matcher:
+  - 'PUBLIC_CLERK_PUBLISHABLE_KEY'
+  - 'PUBLIC_CLERK_DOMAIN'
+  - 'PUBLIC_CLERK_SIGN_IN_URL'
+  - 'PUBLIC_CLERK_SIGN_UP_URL'
+  - 'import.meta.env'
+category: 'behavior-change'
+warning: true
+---
+
+Environment variable resolution in `@clerk/astro` now prefers `process.env` over `import.meta.env`. This means runtime environment variables (e.g., set in the Node.js adapter or container) take precedence over values statically replaced by Vite at build time.
+
+The new resolution order is:
+
+1. `locals.runtime.env` (Cloudflare Workers)
+2. `process.env` (Node.js runtime)
+3. `import.meta.env` (Vite build-time static replacement)
+
+Previously, `import.meta.env` was checked before `process.env`. If you rely on build-time `PUBLIC_*` values that differ from your runtime `process.env`, you may need to update your configuration to ensure the correct values are set in `process.env` at runtime.