diff --git a/.changeset/afraid-buses-pay.md b/.changeset/afraid-buses-pay.md
new file mode 100644
index 0000000000..7571cfbdb2
--- /dev/null
+++ b/.changeset/afraid-buses-pay.md
@@ -0,0 +1,5 @@
+---
+"@react-router/dev": patch
+---
+
+Handle custom `envDir` in Vite config
diff --git a/integration/helpers/vite.ts b/integration/helpers/vite.ts
index 62b6359904..10e04ebd50 100644
--- a/integration/helpers/vite.ts
+++ b/integration/helpers/vite.ts
@@ -58,8 +58,14 @@ export const reactRouterConfig = ({
   `;
 };
 
+type ViteConfigArgs = {
+  port: number;
+  fsAllow?: string[];
+  envDir?: string;
+};
+
 export const viteConfig = {
-  server: async (args: { port: number; fsAllow?: string[] }) => {
+  server: async (args: ViteConfigArgs) => {
     let { port, fsAllow } = args;
     let hmrPort = await getPort();
     let text = dedent`
@@ -72,7 +78,7 @@ export const viteConfig = {
     `;
     return text;
   },
-  basic: async (args: { port: number; fsAllow?: string[] }) => {
+  basic: async (args: ViteConfigArgs) => {
     return dedent`
       import { reactRouter } from "@react-router/dev/vite";
       import { envOnlyMacros } from "vite-env-only";
@@ -80,6 +86,7 @@ export const viteConfig = {
 
       export default {
         ${await viteConfig.server(args)}
+        envDir: ${args.envDir ? `"${args.envDir}"` : "undefined"},
         plugins: [
           reactRouter(),
           envOnlyMacros(),
diff --git a/integration/vite-dotenv-test.ts b/integration/vite-dotenv-test.ts
index dd27b43520..d96fe1df1a 100644
--- a/integration/vite-dotenv-test.ts
+++ b/integration/vite-dotenv-test.ts
@@ -8,73 +8,113 @@ import {
   viteConfig,
 } from "./helpers/vite.js";
 
-let files = {
-  ".env": `
-    ENV_VAR_FROM_DOTENV_FILE=Content from .env file
-  `,
-  "app/routes/dotenv.tsx": String.raw`
-    import { useState, useEffect } from "react";
-    import { useLoaderData } from "react-router";
-
-    export const loader = () => {
-      return {
-        loaderContent: process.env.ENV_VAR_FROM_DOTENV_FILE,
-      }
-    }
+let getFiles = async ({ envDir, port }: { envDir?: string; port: number }) => {
+  let envPath = `${envDir ? `${envDir}/` : ""}.env`;
 
-    export default function DotenvRoute() {
-      const { loaderContent } = useLoaderData();
+  return {
+    "vite.config.js": await viteConfig.basic({ port, envDir }),
+    "server.mjs": EXPRESS_SERVER({ port }),
+    [envPath]: `
+      ENV_VAR_FROM_DOTENV_FILE=Content from ${envPath} file
+    `,
+    "app/routes/dotenv.tsx": String.raw`
+      import { useState, useEffect } from "react";
+      import { useLoaderData } from "react-router";
 
-      const [clientContent, setClientContent] = useState('');
-      useEffect(() => {
-        try {
-          setClientContent("process.env.ENV_VAR_FROM_DOTENV_FILE shouldn't be available on the client, found: " + process.env.ENV_VAR_FROM_DOTENV_FILE);
-        } catch (err) {
-          setClientContent("process.env.ENV_VAR_FROM_DOTENV_FILE not available on the client, which is a good thing");
+      export const loader = () => {
+        return {
+          loaderContent: process.env.ENV_VAR_FROM_DOTENV_FILE,
         }
-      }, []);
-
-      return <>
-        <div data-dotenv-route-loader-content>{loaderContent}</div>
-        <div data-dotenv-route-client-content>{clientContent}</div>
-      </>
-    }
-  `,
+      }
+
+      export default function DotenvRoute() {
+        const { loaderContent } = useLoaderData();
+
+        const [clientContent, setClientContent] = useState('');
+        useEffect(() => {
+          try {
+            setClientContent("process.env.ENV_VAR_FROM_DOTENV_FILE shouldn't be available on the client, found: " + process.env.ENV_VAR_FROM_DOTENV_FILE);
+          } catch (err) {
+            setClientContent("process.env.ENV_VAR_FROM_DOTENV_FILE not available on the client, which is a good thing");
+          }
+        }, []);
+
+        return <>
+          <div data-dotenv-route-loader-content>{loaderContent}</div>
+          <div data-dotenv-route-client-content>{clientContent}</div>
+        </>
+      }
+    `,
+  };
 };
 
-test.describe(async () => {
-  let port: number;
-  let cwd: string;
-  let stop: () => void;
-
-  test.beforeAll(async () => {
-    port = await getPort();
-    cwd = await createProject({
-      "vite.config.js": await viteConfig.basic({ port }),
-      "server.mjs": EXPRESS_SERVER({ port }),
-      ...files,
+test.describe("Vite .env", () => {
+  test.describe("defaults", async () => {
+    let port: number;
+    let cwd: string;
+    let stop: () => void;
+
+    test.beforeAll(async () => {
+      port = await getPort();
+      cwd = await createProject(await getFiles({ port }));
+      stop = await customDev({ cwd, port });
+    });
+    test.afterAll(() => stop());
+
+    test("express", async ({ page }) => {
+      let pageErrors: unknown[] = [];
+      page.on("pageerror", (error) => pageErrors.push(error));
+
+      await page.goto(`http://localhost:${port}/dotenv`, {
+        waitUntil: "networkidle",
+      });
+      expect(pageErrors).toEqual([]);
+
+      let loaderContent = page.locator("[data-dotenv-route-loader-content]");
+      await expect(loaderContent).toHaveText("Content from .env file");
+
+      let clientContent = page.locator("[data-dotenv-route-client-content]");
+      await expect(clientContent).toHaveText(
+        "process.env.ENV_VAR_FROM_DOTENV_FILE not available on the client, which is a good thing"
+      );
+
+      expect(pageErrors).toEqual([]);
     });
-    stop = await customDev({ cwd, port });
   });
-  test.afterAll(() => stop());
 
-  test("Vite / Load context / express", async ({ page }) => {
-    let pageErrors: unknown[] = [];
-    page.on("pageerror", (error) => pageErrors.push(error));
+  test.describe("custom env dir", async () => {
+    let port: number;
+    let cwd: string;
+    let stop: () => void;
 
-    await page.goto(`http://localhost:${port}/dotenv`, {
-      waitUntil: "networkidle",
+    test.beforeAll(async () => {
+      const envDir = "custom-env-dir";
+      port = await getPort();
+      cwd = await createProject(await getFiles({ envDir, port }));
+      stop = await customDev({ cwd, port });
     });
-    expect(pageErrors).toEqual([]);
+    test.afterAll(() => stop());
+
+    test("express", async ({ page }) => {
+      let pageErrors: unknown[] = [];
+      page.on("pageerror", (error) => pageErrors.push(error));
 
-    let loaderContent = page.locator("[data-dotenv-route-loader-content]");
-    await expect(loaderContent).toHaveText("Content from .env file");
+      await page.goto(`http://localhost:${port}/dotenv`, {
+        waitUntil: "networkidle",
+      });
+      expect(pageErrors).toEqual([]);
 
-    let clientContent = page.locator("[data-dotenv-route-client-content]");
-    await expect(clientContent).toHaveText(
-      "process.env.ENV_VAR_FROM_DOTENV_FILE not available on the client, which is a good thing"
-    );
+      let loaderContent = page.locator("[data-dotenv-route-loader-content]");
+      await expect(loaderContent).toHaveText(
+        "Content from custom-env-dir/.env file"
+      );
 
-    expect(pageErrors).toEqual([]);
+      let clientContent = page.locator("[data-dotenv-route-client-content]");
+      await expect(clientContent).toHaveText(
+        "process.env.ENV_VAR_FROM_DOTENV_FILE not available on the client, which is a good thing"
+      );
+
+      expect(pageErrors).toEqual([]);
+    });
   });
 });
diff --git a/packages/react-router-dev/vite/plugin.ts b/packages/react-router-dev/vite/plugin.ts
index a936096288..3ca46360d9 100644
--- a/packages/react-router-dev/vite/plugin.ts
+++ b/packages/react-router-dev/vite/plugin.ts
@@ -955,7 +955,7 @@ export const reactRouterVitePlugin: ReactRouterVitePlugin = () => {
           process.env,
           vite.loadEnv(
             viteConfigEnv.mode,
-            ctx.rootDirectory,
+            viteUserConfig.envDir ?? ctx.rootDirectory,
             // We override default prefix of "VITE_" with a blank string since
             // we're targeting the server, so we want to load all environment
             // variables, not just those explicitly marked for the client