diff --git a/packages/react-doctor/src/cli.ts b/packages/react-doctor/src/cli.ts
index 5b6cec0..58e7497 100644
--- a/packages/react-doctor/src/cli.ts
+++ b/packages/react-doctor/src/cli.ts
@@ -37,6 +37,7 @@ interface CliFlags {
   offline: boolean;
   ami: boolean;
   project?: string;
+  packageJson?: string;
   diff?: boolean | string;
   failOn: string;
 }
@@ -141,6 +142,7 @@ const program = new Command()
   .option("--score", "output only the score")
   .option("-y, --yes", "skip prompts, scan all workspace projects")
   .option("--project <name>", "select workspace project (comma-separated for multiple)")
+  .option("--package-json <directory>", "custom directory containing package.json")
   .option("--diff [base]", "scan only files changed vs base branch")
   .option("--offline", "skip telemetry (anonymous, not stored, only used to calculate score)")
   .option("--no-ami", "skip Ami-related prompts")
@@ -158,13 +160,21 @@ const program = new Command()
         logger.break();
       }
 
-      const scanOptions = resolveCliScanOptions(flags, userConfig, program);
+      const resolvedPackageJsonDirectory = flags.packageJson
+        ? path.resolve(flags.packageJson)
+        : undefined;
+
+      const scanOptions: ScanOptions = {
+        ...resolveCliScanOptions(flags, userConfig, program),
+        packageJsonDirectory: resolvedPackageJsonDirectory,
+      };
       const shouldSkipPrompts = flags.yes || isAutomatedEnvironment() || !process.stdin.isTTY;
       const shouldSkipAmiPrompts = shouldSkipPrompts || !flags.ami;
       const projectDirectories = await selectProjects(
         resolvedDirectory,
         flags.project,
         shouldSkipPrompts,
+        resolvedPackageJsonDirectory,
       );
 
       const isDiffCliOverride = program.getOptionValueSource("diff") === "cli";
diff --git a/packages/react-doctor/src/index.ts b/packages/react-doctor/src/index.ts
index 14384d4..c4ffb89 100644
--- a/packages/react-doctor/src/index.ts
+++ b/packages/react-doctor/src/index.ts
@@ -14,6 +14,7 @@ export { getDiffInfo, filterSourceFiles } from "./utils/get-diff-files.js";
 export interface DiagnoseOptions {
   lint?: boolean;
   deadCode?: boolean;
+  packageJsonDirectory?: string;
   includePaths?: string[];
 }
 
@@ -28,12 +29,15 @@ export const diagnose = async (
   directory: string,
   options: DiagnoseOptions = {},
 ): Promise<DiagnoseResult> => {
-  const { includePaths = [] } = options;
+  const { packageJsonDirectory, includePaths = [] } = options;
   const isDiffMode = includePaths.length > 0;
 
   const startTime = performance.now();
   const resolvedDirectory = path.resolve(directory);
-  const projectInfo = discoverProject(resolvedDirectory);
+  const resolvedPackageJsonDirectory = packageJsonDirectory
+    ? path.resolve(packageJsonDirectory)
+    : undefined;
+  const projectInfo = discoverProject(resolvedDirectory, resolvedPackageJsonDirectory);
   const userConfig = loadConfig(resolvedDirectory);
 
   const effectiveLint = options.lint ?? userConfig?.lint ?? true;
diff --git a/packages/react-doctor/src/scan.ts b/packages/react-doctor/src/scan.ts
index 7dd8749..0d3ad32 100644
--- a/packages/react-doctor/src/scan.ts
+++ b/packages/react-doctor/src/scan.ts
@@ -458,7 +458,7 @@ export const scan = async (
   inputOptions: ScanOptions = {},
 ): Promise<ScanResult> => {
   const startTime = performance.now();
-  const projectInfo = discoverProject(directory);
+  const projectInfo = discoverProject(directory, inputOptions.packageJsonDirectory);
   const userConfig = loadConfig(directory);
   const options = mergeScanOptions(inputOptions, userConfig);
   const { includePaths } = options;
diff --git a/packages/react-doctor/src/types.ts b/packages/react-doctor/src/types.ts
index b0c4827..d02bc8e 100644
--- a/packages/react-doctor/src/types.ts
+++ b/packages/react-doctor/src/types.ts
@@ -113,6 +113,7 @@ export interface ScanOptions {
   scoreOnly?: boolean;
   offline?: boolean;
   includePaths?: string[];
+  packageJsonDirectory?: string;
 }
 
 export interface DiffInfo {
diff --git a/packages/react-doctor/src/utils/discover-project.ts b/packages/react-doctor/src/utils/discover-project.ts
index 30e7529..89554a6 100644
--- a/packages/react-doctor/src/utils/discover-project.ts
+++ b/packages/react-doctor/src/utils/discover-project.ts
@@ -260,8 +260,13 @@ const hasReactDependency = (packageJson: PackageJson): boolean => {
   );
 };
 
-export const discoverReactSubprojects = (rootDirectory: string): WorkspacePackage[] => {
-  if (!fs.existsSync(rootDirectory) || !fs.statSync(rootDirectory).isDirectory()) return [];
+export const discoverReactSubprojects = (
+  rootDirectory: string,
+  packageJsonDirectory?: string,
+): WorkspacePackage[] => {
+  const effectiveDirectory = packageJsonDirectory ?? rootDirectory;
+  if (!fs.existsSync(effectiveDirectory) || !fs.statSync(effectiveDirectory).isDirectory())
+    return [];
 
   const packages: WorkspacePackage[] = [];
 
@@ -274,14 +279,14 @@ export const discoverReactSubprojects = (rootDirectory: string): WorkspacePackag
     }
   }
 
-  const entries = fs.readdirSync(rootDirectory, { withFileTypes: true });
+  const entries = fs.readdirSync(effectiveDirectory, { withFileTypes: true });
 
   for (const entry of entries) {
     if (!entry.isDirectory() || entry.name.startsWith(".") || entry.name === "node_modules") {
       continue;
     }
 
-    const subdirectory = path.join(rootDirectory, entry.name);
+    const subdirectory = path.join(effectiveDirectory, entry.name);
     const packageJsonPath = path.join(subdirectory, "package.json");
     if (!isFile(packageJsonPath)) continue;
 
@@ -295,12 +300,16 @@ export const discoverReactSubprojects = (rootDirectory: string): WorkspacePackag
   return packages;
 };
 
-export const listWorkspacePackages = (rootDirectory: string): WorkspacePackage[] => {
-  const packageJsonPath = path.join(rootDirectory, "package.json");
+export const listWorkspacePackages = (
+  rootDirectory: string,
+  packageJsonDirectory?: string,
+): WorkspacePackage[] => {
+  const effectiveDirectory = packageJsonDirectory ?? rootDirectory;
+  const packageJsonPath = path.join(effectiveDirectory, "package.json");
   if (!isFile(packageJsonPath)) return [];
 
   const packageJson = readPackageJson(packageJsonPath);
-  const patterns = getWorkspacePatterns(rootDirectory, packageJson);
+  const patterns = getWorkspacePatterns(effectiveDirectory, packageJson);
   if (patterns.length === 0) return [];
 
   const packages: WorkspacePackage[] = [];
@@ -359,17 +368,21 @@ const detectReactCompiler = (directory: string, packageJson: PackageJson): boole
   return false;
 };
 
-export const discoverProject = (directory: string): ProjectInfo => {
-  const packageJsonPath = path.join(directory, "package.json");
+export const discoverProject = (
+  directory: string,
+  packageJsonDirectory?: string,
+): ProjectInfo => {
+  const packageJsonDir = packageJsonDirectory ?? directory;
+  const packageJsonPath = path.join(packageJsonDir, "package.json");
   if (!isFile(packageJsonPath)) {
-    throw new Error(`No package.json found in ${directory}`);
+    throw new Error(`No package.json found in ${packageJsonDir}`);
   }
 
   const packageJson = readPackageJson(packageJsonPath);
   let { reactVersion, framework } = extractDependencyInfo(packageJson);
 
   if (!reactVersion || framework === "unknown") {
-    const workspaceInfo = findReactInWorkspaces(directory, packageJson);
+    const workspaceInfo = findReactInWorkspaces(packageJsonDir, packageJson);
     if (!reactVersion && workspaceInfo.reactVersion) {
       reactVersion = workspaceInfo.reactVersion;
     }
@@ -378,8 +391,8 @@ export const discoverProject = (directory: string): ProjectInfo => {
     }
   }
 
-  if ((!reactVersion || framework === "unknown") && !isMonorepoRoot(directory)) {
-    const monorepoInfo = findDependencyInfoFromMonorepoRoot(directory);
+  if ((!reactVersion || framework === "unknown") && !isMonorepoRoot(packageJsonDir)) {
+    const monorepoInfo = findDependencyInfoFromMonorepoRoot(packageJsonDir);
     if (!reactVersion) {
       reactVersion = monorepoInfo.reactVersion;
     }
diff --git a/packages/react-doctor/src/utils/select-projects.ts b/packages/react-doctor/src/utils/select-projects.ts
index 9bbc303..021fb15 100644
--- a/packages/react-doctor/src/utils/select-projects.ts
+++ b/packages/react-doctor/src/utils/select-projects.ts
@@ -9,10 +9,11 @@ export const selectProjects = async (
   rootDirectory: string,
   projectFlag: string | undefined,
   skipPrompts: boolean,
+  packageJsonDirectory?: string,
 ): Promise<string[]> => {
-  let packages = listWorkspacePackages(rootDirectory);
+  let packages = listWorkspacePackages(rootDirectory, packageJsonDirectory);
   if (packages.length === 0) {
-    packages = discoverReactSubprojects(rootDirectory);
+    packages = discoverReactSubprojects(rootDirectory, packageJsonDirectory);
   }
 
   if (packages.length === 0) return [rootDirectory];
diff --git a/packages/react-doctor/tests/discover-project.test.ts b/packages/react-doctor/tests/discover-project.test.ts
index 44f9182..b273d6b 100644
--- a/packages/react-doctor/tests/discover-project.test.ts
+++ b/packages/react-doctor/tests/discover-project.test.ts
@@ -12,6 +12,12 @@ import {
 const FIXTURES_DIRECTORY = path.resolve(import.meta.dirname, "fixtures");
 const VALID_FRAMEWORKS = ["nextjs", "vite", "cra", "remix", "gatsby", "unknown"];
 
+const tempDirectory = fs.mkdtempSync(path.join(os.tmpdir(), "react-doctor-discover-test-"));
+
+afterAll(() => {
+  fs.rmSync(tempDirectory, { recursive: true, force: true });
+});
+
 describe("discoverProject", () => {
   it("detects React version from package.json", () => {
     const projectInfo = discoverProject(path.join(FIXTURES_DIRECTORY, "basic-react"));
@@ -44,9 +50,57 @@ describe("discoverProject", () => {
 
     expect(() => discoverProject(projectDirectory)).toThrow("No package.json found");
   });
+
+  describe("with packageJsonDirectory", () => {
+    const sourceDirectory = path.join(FIXTURES_DIRECTORY, "split-project", "source");
+    const metadataDirectory = path.join(FIXTURES_DIRECTORY, "split-project", "metadata");
+
+    it("reads package.json from the custom directory", () => {
+      const projectInfo = discoverProject(sourceDirectory, metadataDirectory);
+      expect(projectInfo.reactVersion).toBe("^19.0.0");
+      expect(projectInfo.projectName).toBe("test-split-project");
+    });
+
+    it("detects tsconfig from the scan directory, not the package.json directory", () => {
+      const projectInfo = discoverProject(sourceDirectory, metadataDirectory);
+      expect(projectInfo.hasTypeScript).toBe(true);
+    });
+
+    it("uses the scan directory as rootDirectory", () => {
+      const projectInfo = discoverProject(sourceDirectory, metadataDirectory);
+      expect(projectInfo.rootDirectory).toBe(sourceDirectory);
+    });
+
+    it("throws when the custom directory has no package.json", () => {
+      expect(() => discoverProject(sourceDirectory, "/nonexistent/path")).toThrow(
+        "No package.json found",
+      );
+    });
+
+    it("falls back to scan directory when packageJsonDirectory is undefined", () => {
+      const projectInfo = discoverProject(path.join(FIXTURES_DIRECTORY, "basic-react"), undefined);
+      expect(projectInfo.reactVersion).toBe("^19.0.0");
+    });
+  });
 });
 
 describe("listWorkspacePackages", () => {
+  it("returns empty when packageJsonDirectory has no package.json", () => {
+    const packages = listWorkspacePackages("/some/root", "/nonexistent/path");
+    expect(packages).toEqual([]);
+  });
+
+  it("returns empty when packageJsonDirectory has no workspaces", () => {
+    const metadataDirectory = path.join(FIXTURES_DIRECTORY, "split-project", "metadata");
+    const packages = listWorkspacePackages("/some/root", metadataDirectory);
+    expect(packages).toEqual([]);
+  });
+
+  it("falls back to rootDirectory when packageJsonDirectory is undefined", () => {
+    const packages = listWorkspacePackages(path.join(FIXTURES_DIRECTORY, "basic-react"));
+    expect(packages).toEqual([]);
+  });
+
   it("resolves nested workspace patterns like apps/*/ClientApp", () => {
     const packages = listWorkspacePackages(path.join(FIXTURES_DIRECTORY, "nested-workspaces"));
     const packageNames = packages.map((workspacePackage) => workspacePackage.name);
@@ -57,12 +111,6 @@ describe("listWorkspacePackages", () => {
   });
 });
 
-const tempDirectory = fs.mkdtempSync(path.join(os.tmpdir(), "react-doctor-discover-test-"));
-
-afterAll(() => {
-  fs.rmSync(tempDirectory, { recursive: true, force: true });
-});
-
 describe("discoverReactSubprojects", () => {
   it("skips subdirectories where package.json is a directory (EISDIR)", () => {
     const rootDirectory = path.join(tempDirectory, "eisdir-package-json");
@@ -134,6 +182,23 @@ describe("discoverReactSubprojects", () => {
     const packages = discoverReactSubprojects(rootDirectory);
     expect(packages).toHaveLength(1);
   });
+
+  it("returns empty when packageJsonDirectory does not exist", () => {
+    const packages = discoverReactSubprojects("/some/root", "/nonexistent/path");
+    expect(packages).toEqual([]);
+  });
+
+  it("scans the packageJsonDirectory for subprojects instead of rootDirectory", () => {
+    const packages = discoverReactSubprojects("/nonexistent/root", FIXTURES_DIRECTORY);
+    const names = packages.map((p) => p.name);
+    expect(names).toContain("test-basic-react");
+  });
+
+  it("falls back to rootDirectory when packageJsonDirectory is undefined", () => {
+    const packages = discoverReactSubprojects(FIXTURES_DIRECTORY);
+    const names = packages.map((p) => p.name);
+    expect(names).toContain("test-basic-react");
+  });
 });
 
 describe("formatFrameworkName", () => {
diff --git a/packages/react-doctor/tests/fixtures/split-project/metadata/package.json b/packages/react-doctor/tests/fixtures/split-project/metadata/package.json
new file mode 100644
index 0000000..01c3c69
--- /dev/null
+++ b/packages/react-doctor/tests/fixtures/split-project/metadata/package.json
@@ -0,0 +1,8 @@
+{
+  "name": "test-split-project",
+  "private": true,
+  "dependencies": {
+    "react": "^19.0.0",
+    "react-dom": "^19.0.0"
+  }
+}
diff --git a/packages/react-doctor/tests/fixtures/split-project/source/src/app.tsx b/packages/react-doctor/tests/fixtures/split-project/source/src/app.tsx
new file mode 100644
index 0000000..9f8c81e
--- /dev/null
+++ b/packages/react-doctor/tests/fixtures/split-project/source/src/app.tsx
@@ -0,0 +1 @@
+export const App = () => <div>Hello</div>;
diff --git a/packages/react-doctor/tests/fixtures/split-project/source/tsconfig.json b/packages/react-doctor/tests/fixtures/split-project/source/tsconfig.json
new file mode 100644
index 0000000..1e15af6
--- /dev/null
+++ b/packages/react-doctor/tests/fixtures/split-project/source/tsconfig.json
@@ -0,0 +1,9 @@
+{
+  "compilerOptions": {
+    "jsx": "react-jsx",
+    "strict": true,
+    "target": "ESNext",
+    "module": "ESNext",
+    "moduleResolution": "bundler"
+  }
+}
diff --git a/packages/react-doctor/tests/scan.test.ts b/packages/react-doctor/tests/scan.test.ts
index 7bf6875..8ec8673 100644
--- a/packages/react-doctor/tests/scan.test.ts
+++ b/packages/react-doctor/tests/scan.test.ts
@@ -66,6 +66,34 @@ describe("scan", () => {
     }
   });
 
+  it("reads package.json from packageJsonDirectory when provided", async () => {
+    const consoleSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    try {
+      await scan(path.join(FIXTURES_DIRECTORY, "split-project", "source"), {
+        lint: false,
+        deadCode: false,
+        packageJsonDirectory: path.join(FIXTURES_DIRECTORY, "split-project", "metadata"),
+      });
+    } finally {
+      consoleSpy.mockRestore();
+    }
+  });
+
+  it("throws when packageJsonDirectory has no React dependency", async () => {
+    const consoleSpy = vi.spyOn(console, "log").mockImplementation(() => {});
+    try {
+      await expect(
+        scan(path.join(FIXTURES_DIRECTORY, "basic-react"), {
+          lint: false,
+          deadCode: false,
+          packageJsonDirectory: noReactTempDirectory,
+        }),
+      ).rejects.toThrow("No React dependency found");
+    } finally {
+      consoleSpy.mockRestore();
+    }
+  });
+
   it("runs lint and dead code in parallel when both enabled", async () => {
     const consoleSpy = vi.spyOn(console, "log").mockImplementation(() => {});
     try {