diff --git a/.changeset/server-functions-real-root.md b/.changeset/server-functions-real-root.md
new file mode 100644
index 000000000..cefb7cfbe
--- /dev/null
+++ b/.changeset/server-functions-real-root.md
@@ -0,0 +1,5 @@
+---
+"@solidjs/start": patch
+---
+
+Resolve the server function filter and the ids of lazily loaded modules against Vite's root instead of the working directory. On Windows a working directory entered through a junction or symlink keeps that path, while Vite (8.2 and later) resolves the root and every module id to the real path. The filter then matched no module, so no `"use server"` function was compiled: its body shipped in the client bundle, and the build failed with `Attempt to import 'server-only' in a client module` once one of them imported server-only code such as `@solidjs/start/http`. The ids of lazily loaded route components matched no client manifest entry either, so their CSS was missing from the server-rendered HTML. Relative patterns in the `serverFunctions.filter` option now resolve against Vite's root too.
diff --git a/packages/start/src/config/lazy.spec.ts b/packages/start/src/config/lazy.spec.ts
index 39adb2fad..2e7e18ef8 100644
--- a/packages/start/src/config/lazy.spec.ts
+++ b/packages/start/src/config/lazy.spec.ts
@@ -1,13 +1,21 @@
-import { describe, expect, it } from "vitest";
+import { afterEach, describe, expect, it, vi } from "vitest";
 
 import lazy from "./lazy.ts";
 
-async function transform(code: string, id = `${process.cwd()}/src/routes/page.tsx`) {
+async function transform(
+  code: string,
+  id = `${process.cwd()}/src/routes/page.tsx`,
+  root = process.cwd(),
+) {
   const plugin = lazy() as any;
-  const context = { environment: { name: "ssr" } };
+  const context = { environment: { name: "ssr", config: { root } } };
   return plugin.transform.call(context, code, id);
 }
 
+afterEach(() => {
+  vi.restoreAllMocks();
+});
+
 describe("lazy", () => {
   it("appends the module id without moving existing code", async () => {
     const code = `import { A } from "./a.ts";\nexport default function Page() { return A; }`;
@@ -29,6 +37,19 @@ describe("lazy", () => {
     expect(result.map).toBeTruthy();
   });
 
+  it("names the module relative to the root when the working directory is a link to it", async () => {
+    // Vite (8.2 and later) resolves its root and module ids to the real path.
+    // On Windows the working directory keeps the junction or symlink path.
+    vi.spyOn(process, "cwd").mockReturnValue("/link/app");
+    const result = await transform(
+      `import { A } from "./a.ts";\nexport default A;`,
+      "/real/app/src/routes/page.tsx",
+      "/real/app",
+    );
+
+    expect(result.code).toContain(`export const id$$ = "src/routes/page.tsx";`);
+  });
+
   it("skips a module without a default export or lazy", async () => {
     expect(await transform(`import { A } from "./a.ts";\nexport const B = A;`)).toBeUndefined();
   });
diff --git a/packages/start/src/config/lazy.ts b/packages/start/src/config/lazy.ts
index 72fbfc3d2..7518817e1 100644
--- a/packages/start/src/config/lazy.ts
+++ b/packages/start/src/config/lazy.ts
@@ -1,9 +1,9 @@
 import type { PluginItem } from "@babel/core";
 import babel from "@babel/core";
 import * as t from "@babel/types";
-import { sep as osSep } from "node:path";
-import { basename, relative, sep } from "node:path/posix";
-import type { PluginOption } from "vite";
+import { relative } from "node:path";
+import { basename } from "node:path/posix";
+import { normalizePath, type PluginOption } from "vite";
 import { VITE_ENVIRONMENTS } from "./constants.ts";
 
 const importTransform = (): PluginItem => {
@@ -31,8 +31,6 @@ const importTransform = (): PluginItem => {
 const fileEndingRegex = /(ts|js)x(\?.*)?$/;
 
 const lazy = (): PluginOption => {
-  const cwd = process.cwd().replaceAll(osSep, sep);
-
   /**
    * Maps module ids to their client-specific shared chunk names.
    * Modules in shared chunks need to find their assets via the chunk name, instead of their module id.
@@ -84,7 +82,11 @@ const lazy = (): PluginOption => {
       // source map of the input still applies to the output.
       let idExport = "";
       if (src.indexOf("export default") !== -1) {
-        const chunkName = sharedChunkNames[id] ?? relative(cwd, id);
+        // Derived the way Vite derives the client manifest keys it is looked
+        // up by. Relative to the working directory, it would match no key when
+        // that directory reaches the project through a junction or symlink.
+        const chunkName =
+          sharedChunkNames[id] ?? normalizePath(relative(this.environment.config.root, id));
         idExport = `\nexport const id$$ = ${JSON.stringify(chunkName)};\n`;
       }
 
diff --git a/packages/start/src/directives/index.spec.ts b/packages/start/src/directives/index.spec.ts
new file mode 100644
index 000000000..a84158b78
--- /dev/null
+++ b/packages/start/src/directives/index.spec.ts
@@ -0,0 +1,64 @@
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { normalizePath } from "vite";
+import { afterEach, describe, expect, it, vi } from "vitest";
+
+import { type ServerFunctionsFilter, serverFunctionsPlugin } from "./index.ts";
+
+// Vite (8.2 and later) resolves its root and every module id to the real path.
+// On Windows the working directory keeps the path it was entered through, so it
+// can name the same project through a junction or symlink.
+const root = normalizePath(join(tmpdir(), "solid-start-app"));
+const linkedRoot = normalizePath(join(tmpdir(), "solid-start-link"));
+
+const code = `
+export async function getMessage() {
+  "use server";
+  return "hello";
+}
+`;
+
+function clientTransform(filter?: ServerFunctionsFilter) {
+  const plugins = serverFunctionsPlugin({
+    manifest: "virtual:server-fn-manifest",
+    runtime: { server: "virtual:server-runtime", client: "virtual:client-runtime" },
+    filter,
+  }) as any[];
+  for (const plugin of plugins) plugin.configResolved?.({ root, mode: "production" });
+
+  const compiler = plugins.find(p => p.name === "solid-start:server-functions/compiler");
+  const context = { environment: { config: { consumer: "client" } }, warn() {} };
+  return (id: string) => compiler.transform.call(context, code, id);
+}
+
+afterEach(() => {
+  vi.restoreAllMocks();
+});
+
+describe("serverFunctionsPlugin", () => {
+  it("compiles server functions when the working directory is a link to the root", async () => {
+    vi.spyOn(process, "cwd").mockReturnValue(linkedRoot);
+    const transform = clientTransform();
+
+    const result = await transform(`${root}/src/message.ts`);
+
+    expect(result).not.toBeNull();
+    expect(result.code).toContain("virtual:client-runtime");
+    expect(result.code).not.toContain("hello");
+  });
+
+  it("leaves modules outside the root's src folder alone", async () => {
+    vi.spyOn(process, "cwd").mockReturnValue(linkedRoot);
+    const transform = clientTransform();
+
+    expect(await transform(`${root}/scripts/message.ts`)).toBeNull();
+  });
+
+  it("resolves relative filter patterns against the root", async () => {
+    vi.spyOn(process, "cwd").mockReturnValue(linkedRoot);
+    const transform = clientTransform({ include: "app/**/*.ts" });
+
+    expect(await transform(`${root}/app/message.ts`)).not.toBeNull();
+    expect(await transform(`${root}/src/message.ts`)).toBeNull();
+  });
+});
diff --git a/packages/start/src/directives/index.ts b/packages/start/src/directives/index.ts
index 62137e271..2926b938a 100644
--- a/packages/start/src/directives/index.ts
+++ b/packages/start/src/directives/index.ts
@@ -125,10 +125,7 @@ function invalidateModules(
 }
 
 export function serverFunctionsPlugin(options: ServerFunctionsOptions): Plugin[] {
-  const filter = createFilter(
-    options.filter?.include || DEFAULT_INCLUDE,
-    options.filter?.exclude || DEFAULT_EXCLUDE,
-  );
+  let filter: ReturnType<typeof createFilter>;
 
   let env: CompileOptions["env"];
 
@@ -177,6 +174,15 @@ export function serverFunctionsPlugin(options: ServerFunctionsOptions): Plugin[]
       enforce: "pre",
       configResolved(config) {
         env = config.mode !== "production" ? "development" : "production";
+        // Vite resolves its root like every module id: to the real path since
+        // Vite 8.2, unless `resolve.preserveSymlinks`. Patterns resolved against
+        // a working directory that reaches the project through a junction or
+        // symlink would match no module.
+        filter = createFilter(
+          options.filter?.include || DEFAULT_INCLUDE,
+          options.filter?.exclude || DEFAULT_EXCLUDE,
+          { resolve: config.root },
+        );
       },
       configureServer(server) {
         currentServer = server;
diff --git a/packages/start/src/server/collect-styles.spec.ts b/packages/start/src/server/collect-styles.spec.ts
new file mode 100644
index 000000000..08f449c13
--- /dev/null
+++ b/packages/start/src/server/collect-styles.spec.ts
@@ -0,0 +1,37 @@
+import { tmpdir } from "node:os";
+import { join, resolve } from "node:path";
+import { normalizePath } from "vite";
+import { afterEach, describe, expect, it, vi } from "vitest";
+
+import { findStylesInModuleGraph } from "./collect-styles.ts";
+
+afterEach(() => {
+  vi.restoreAllMocks();
+});
+
+describe("findStylesInModuleGraph", () => {
+  it("resolves the id against the root when the working directory is a link to it", async () => {
+    const root = join(tmpdir(), "solid-start-app");
+    vi.spyOn(process, "cwd").mockReturnValue(join(tmpdir(), "solid-start-link"));
+    const page = resolve(root, "src/routes/page.tsx");
+    const style = resolve(root, "src/routes/page.css");
+    const modules: Record<string, object> = {
+      [page]: {
+        id: page,
+        url: "/src/routes/page.tsx",
+        file: page,
+        transformResult: { deps: [style] },
+      },
+      [style]: { id: style, url: "/src/routes/page.css", file: style },
+    };
+    const environment = {
+      config: { root: normalizePath(root) },
+      fetchModule: async (file: string) => (file in modules ? { id: file } : {}),
+      moduleGraph: { getModuleById: (id: string) => modules[id] },
+    } as any;
+
+    const styles = await findStylesInModuleGraph(environment, "src/routes/page.tsx", () => true);
+
+    expect(styles).toEqual({ [style]: "/src/routes/page.css" });
+  });
+});
diff --git a/packages/start/src/server/collect-styles.ts b/packages/start/src/server/collect-styles.ts
index bb9510bde..affc954f4 100644
--- a/packages/start/src/server/collect-styles.ts
+++ b/packages/start/src/server/collect-styles.ts
@@ -60,7 +60,8 @@ export async function findStylesInModuleGraph(
   id: string,
   filter: StyleFilter,
 ) {
-  const absolute = path.resolve(process.cwd(), id);
+  // Ids are relative to Vite's root, as `lazy` derives `id$$`.
+  const absolute = path.resolve(vite.config.root, id);
   const dependencies = new Set<EnvironmentModuleNode>();
 
   try {