diff --git a/src/bundler/linker_context/postProcessCSSChunk.zig b/src/bundler/linker_context/postProcessCSSChunk.zig
index e3f680676c..7941bebac5 100644
--- a/src/bundler/linker_context/postProcessCSSChunk.zig
+++ b/src/bundler/linker_context/postProcessCSSChunk.zig
@@ -105,7 +105,7 @@ pub fn postProcessCSSChunk(ctx: GenerateChunkCtx, worker: *ThreadPool.Worker, ch
             chunk.isolated_hash,
             worker,
             compile_results_for_source_map,
-            c.resolver.opts.output_dir,
+            c.resolver.opts.root_dir,
             can_have_shifts,
         );
     }
diff --git a/src/bundler/linker_context/postProcessJSChunk.zig b/src/bundler/linker_context/postProcessJSChunk.zig
index bfe0035a44..14541ed6b0 100644
--- a/src/bundler/linker_context/postProcessJSChunk.zig
+++ b/src/bundler/linker_context/postProcessJSChunk.zig
@@ -429,7 +429,7 @@ pub fn postProcessJSChunk(ctx: GenerateChunkCtx, worker: *ThreadPool.Worker, chu
             chunk.isolated_hash,
             worker,
             compile_results_for_source_map,
-            c.resolver.opts.output_dir,
+            c.resolver.opts.root_dir,
             can_have_shifts,
         );
     }
diff --git a/test/regression/issue/3332.test.ts b/test/regression/issue/3332.test.ts
new file mode 100644
index 0000000000..f358111c94
--- /dev/null
+++ b/test/regression/issue/3332.test.ts
@@ -0,0 +1,68 @@
+import { describe, expect, test } from "bun:test";
+import { tempDir } from "harness";
+import path from "path";
+
+describe("issue #3332 - sourcemap sources should be relative to root", () => {
+  test("JS sourcemap sources are relative to root, not output directory", async () => {
+    using dir = tempDir("issue-3332-js", {
+      "src/index.ts": `import { helper } from './nested/helper';
+console.log(helper());`,
+      "src/nested/helper.ts": `export function helper() {
+  return 'hello';
+}`,
+    });
+
+    const result = await Bun.build({
+      entrypoints: [path.join(String(dir), "src/index.ts")],
+      outdir: path.join(String(dir), "dist"),
+      root: String(dir),
+      sourcemap: "external",
+    });
+
+    expect(result.success).toBe(true);
+
+    // Find the sourcemap output
+    const sourcemapOutput = result.outputs.find(o => o.kind === "sourcemap");
+    expect(sourcemapOutput).toBeDefined();
+
+    // Parse the sourcemap
+    const mapContent = await sourcemapOutput!.text();
+    const map = JSON.parse(mapContent);
+
+    // Sources should be relative to root (the project directory), not output directory
+    // Expected: ["src/nested/helper.ts", "src/index.ts"] (or similar)
+    // Bug behavior: ["../src/nested/helper.ts", "../src/index.ts"] (relative to dist/src/)
+    for (const source of map.sources) {
+      expect(source).not.toMatch(/^\.\.\//);
+      expect(source).toMatch(/^src\//);
+    }
+
+    expect(map.sources).toContain("src/index.ts");
+    expect(map.sources).toContain("src/nested/helper.ts");
+  });
+
+  test("sourcemap sources without explicit root use cwd", async () => {
+    using dir = tempDir("issue-3332-no-root", {
+      "index.ts": `console.log('hello');`,
+    });
+
+    const result = await Bun.build({
+      entrypoints: [path.join(String(dir), "index.ts")],
+      outdir: path.join(String(dir), "dist"),
+      sourcemap: "external",
+    });
+
+    expect(result.success).toBe(true);
+
+    const sourcemapOutput = result.outputs.find(o => o.kind === "sourcemap");
+    expect(sourcemapOutput).toBeDefined();
+
+    const mapContent = await sourcemapOutput!.text();
+    const map = JSON.parse(mapContent);
+
+    // Sources should contain just the filename or a relative path, not "../"
+    for (const source of map.sources) {
+      expect(source).not.toMatch(/^\.\.\//);
+    }
+  });
+});