diff --git a/README.md b/README.md
index 46f0a6d..08c1e09 100644
--- a/README.md
+++ b/README.md
@@ -34,7 +34,7 @@ To use this server, you must have both Python and [Deno](https://deno.com/) inst
 The server can be run with `deno` installed using `uvx`:
 
 ```bash
-uvx mcp-run-python [-h] [--version] [--port PORT] [--deps DEPS] {stdio,streamable-http,streamable-http-stateless,example}
+uvx mcp-run-python [-h] [--version] [--port PORT] [--dep PKG]... [--index-url URL]... {stdio,streamable-http,streamable-http-stateless,example}
 ```
 
 where:
@@ -49,7 +49,7 @@ where:
 - `streamable-http-stateless` runs the server with [Streamable HTTP MCP transport](https://modelcontextprotocol.io/specification/2025-06-18/basic/transports#streamable-http) in stateless mode and does not
   support server-to-client notifications
 - `example` will run a minimal Python script using `numpy`, useful for checking that the package is working, for the code
-  to run successfully, you'll need to install `numpy` using `uvx mcp-run-python --deps numpy example`
+  to run successfully, you'll need to install `numpy` using `uvx mcp-run-python --dep numpy example`
 
 ## Usage with Pydantic AI
 
@@ -166,3 +166,13 @@ edit the filesystem.
 * `deno` is then run with read-only permissions to the `node_modules` directory to run untrusted code.
 
 Dependencies must be provided when initializing the server so they can be installed in the first step.
+
+## Custom Package Indexes
+
+Use `--index-url` to install dependencies from private registries (can be repeated, tried in order before PyPI):
+
+```bash
+uvx mcp-run-python --index-url https://private.repo.com/simple --dep mypackage stdio
+```
+
+The Python API accepts `index_urls` in `code_sandbox`, `prepare_deno_env`, and `run_mcp_server`. See [micropip documentation](https://micropip.pyodide.org/en/stable/project/api.html#micropip.install) for index URL requirements.
diff --git a/build/prepare_env.py b/build/prepare_env.py
index 492101d..7b5901e 100644
--- a/build/prepare_env.py
+++ b/build/prepare_env.py
@@ -31,7 +31,7 @@ class Error:
     kind: Literal['error'] = 'error'
 
 
-async def prepare_env(dependencies: list[str] | None) -> Success | Error:
+async def prepare_env(dependencies: list[str] | None, index_urls: list[str] | None = None) -> Success | Error:
     sys.setrecursionlimit(400)
 
     if dependencies:
@@ -39,7 +39,7 @@ async def prepare_env(dependencies: list[str] | None) -> Success | Error:
 
         with _micropip_logging() as logs_filename:
             try:
-                await micropip.install(dependencies, keep_going=True)
+                await micropip.install(dependencies, keep_going=True, index_urls=index_urls or None)
                 importlib.invalidate_caches()
             except Exception:
                 with open(logs_filename) as f:
diff --git a/mcp_run_python/_cli.py b/mcp_run_python/_cli.py
index 69bab42..40f8744 100644
--- a/mcp_run_python/_cli.py
+++ b/mcp_run_python/_cli.py
@@ -3,6 +3,7 @@
 import argparse
 import logging
 import sys
+import warnings
 from collections.abc import Sequence
 
 from . import __version__
@@ -22,7 +23,17 @@ def cli_logic(args_list: Sequence[str] | None = None) -> int:
     )
 
     parser.add_argument('--port', type=int, help='Port to run the server on, default 3001.')
-    parser.add_argument('--deps', '--dependencies', help='Comma separated list of dependencies to install')
+    parser.add_argument(
+        '--dep', action='append', dest='dep_list', metavar='PKG', help='Dependency to install (can be repeated)'
+    )
+    parser.add_argument('--deps', '--dependencies', help=argparse.SUPPRESS)
+    parser.add_argument(
+        '--index-url',
+        action='append',
+        dest='index_urls',
+        metavar='URL',
+        help='Package index URL for installing dependencies (can be repeated, tried in order before PyPI)',
+    )
     parser.add_argument(
         '--disable-networking', action='store_true', help='Disable networking during execution of python code'
     )
@@ -46,12 +57,21 @@ def cli_logic(args_list: Sequence[str] | None = None) -> int:
             format='%(message)s',
         )
 
-        deps: list[str] = args.deps.split(',') if args.deps else []
+        deps: list[str] = args.dep_list or []
+        if args.deps:
+            warnings.warn(
+                '--deps is deprecated, use --dep instead (can be repeated)',
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            deps.extend(args.deps.split(','))
+        index_urls: list[str] = args.index_urls or []
         return_code = run_mcp_server(
             args.mode.replace('-', '_'),
             allow_networking=not args.disable_networking,
             http_port=args.port,
             dependencies=deps,
+            index_urls=index_urls,
             deps_log_handler=deps_log_handler,
             verbose=bool(args.verbose),
         )
diff --git a/mcp_run_python/code_sandbox.py b/mcp_run_python/code_sandbox.py
index f552861..1f09030 100644
--- a/mcp_run_python/code_sandbox.py
+++ b/mcp_run_python/code_sandbox.py
@@ -54,6 +54,7 @@ async def eval(
 async def code_sandbox(
     *,
     dependencies: list[str] | None = None,
+    index_urls: list[str] | None = None,
     log_handler: LogHandler | None = None,
     allow_networking: bool = True,
 ) -> AsyncIterator['CodeSandbox']:
@@ -61,6 +62,7 @@ async def code_sandbox(
 
     Args:
         dependencies: A list of dependencies to be installed.
+        index_urls: Package index URLs for installing dependencies (tried in order before PyPI).
         log_handler: A callback function to handle print statements when code is running.
         deps_log_handler: A callback function to run on log statements during initial install of dependencies.
         allow_networking: Whether to allow networking or not while executing python code.
@@ -68,6 +70,7 @@ async def code_sandbox(
     async with async_prepare_deno_env(
         'stdio',
         dependencies=dependencies,
+        index_urls=index_urls,
         deps_log_handler=log_handler,
         return_mode='json',
         allow_networking=allow_networking,
diff --git a/mcp_run_python/deno/src/main.ts b/mcp_run_python/deno/src/main.ts
index f71ccbd..7b131eb 100644
--- a/mcp_run_python/deno/src/main.ts
+++ b/mcp_run_python/deno/src/main.ts
@@ -21,26 +21,37 @@ export async function main() {
   const { args } = Deno
   const flags = parseArgs(Deno.args, {
     string: ['deps', 'return-mode', 'port'],
+    collect: ['dep', 'index-url'],
     default: { port: '3001', 'return-mode': 'xml' },
   })
-  const deps = flags.deps?.split(',') ?? []
+
+  // Deprecation warnings for old comma-separated args
+  if (flags.deps) {
+    console.warn('Warning: --deps is deprecated, use --dep instead (can be repeated)')
+  }
+  // Support both new repeatable args and old comma-separated (backwards compat)
+  const deps: string[] = [
+    ...((flags.dep as string[] | undefined) ?? []),
+    ...(flags.deps?.split(',').filter(Boolean) ?? []),
+  ]
+  const indexUrls: string[] = (flags['index-url'] as string[] | undefined) ?? []
   if (args.length >= 1) {
     if (args[0] === 'stdio') {
-      await runStdio(deps, flags['return-mode'])
+      await runStdio(deps, indexUrls, flags['return-mode'])
       return
     } else if (args[0] === 'streamable_http') {
       const port = parseInt(flags.port)
-      runStreamableHttp(port, deps, flags['return-mode'], false)
+      runStreamableHttp(port, deps, indexUrls, flags['return-mode'], false)
       return
     } else if (args[0] === 'streamable_http_stateless') {
       const port = parseInt(flags.port)
-      runStreamableHttp(port, deps, flags['return-mode'], true)
+      runStreamableHttp(port, deps, indexUrls, flags['return-mode'], true)
       return
     } else if (args[0] === 'example') {
-      await example(deps)
+      await example(deps, indexUrls)
       return
     } else if (args[0] === 'noop') {
-      await installDeps(deps)
+      await installDeps(deps, indexUrls)
       return
     }
   }
@@ -51,9 +62,10 @@ Invalid arguments: ${args.join(' ')}
 Usage: deno ... deno/main.ts [stdio|streamable_http|streamable_http_stateless|example|noop]
 
 options:
---port <port>             Port to run the HTTP server on (default: 3001)
---deps <deps>             Comma separated list of dependencies to install
---return-mode <xml/json>  Return mode for output data (default: xml)`,
+--port <port>               Port to run the HTTP server on (default: 3001)
+--dep <pkg>                 Dependency to install (can be repeated)
+--index-url <url>           Package index URL (can be repeated, tried before PyPI)
+--return-mode <xml/json>    Return mode for output data (default: xml)`,
   )
   Deno.exit(1)
 }
@@ -61,7 +73,7 @@ options:
 /*
  * Create an MCP server with the `run_python_code` tool registered.
  */
-function createServer(deps: string[], returnMode: string): McpServer {
+function createServer(deps: string[], indexUrls: string[], returnMode: string): McpServer {
   const runCode = new RunCode()
   const server = new McpServer(
     {
@@ -106,6 +118,7 @@ The code will be executed with Python 3.13.
       const logPromises: Promise<void>[] = []
       const result = await runCode.run(
         deps,
+        indexUrls,
         (level, data) => {
           if (LogLevels.indexOf(level) >= LogLevels.indexOf(setLogLevel)) {
             logPromises.push(server.server.sendLoggingMessage({ level, data }))
@@ -171,14 +184,20 @@ function httpSetJsonResponse(res: http.ServerResponse, status: number, text: str
 /*
  * Run the MCP server using the Streamable HTTP transport
  */
-function runStreamableHttp(port: number, deps: string[], returnMode: string, stateless: boolean): void {
-  const server = (stateless ? createStatelessHttpServer : createStatefulHttpServer)(deps, returnMode)
+function runStreamableHttp(
+  port: number,
+  deps: string[],
+  indexUrls: string[],
+  returnMode: string,
+  stateless: boolean,
+): void {
+  const server = (stateless ? createStatelessHttpServer : createStatefulHttpServer)(deps, indexUrls, returnMode)
   server.listen(port, () => {
     console.log(`Listening on port ${port}`)
   })
 }
 
-function createStatelessHttpServer(deps: string[], returnMode: string): http.Server {
+function createStatelessHttpServer(deps: string[], indexUrls: string[], returnMode: string): http.Server {
   return http.createServer(async (req, res) => {
     const url = httpGetUrl(req)
 
@@ -188,7 +207,7 @@ function createStatelessHttpServer(deps: string[], returnMode: string): http.Ser
     }
 
     try {
-      const mcpServer = createServer(deps, returnMode)
+      const mcpServer = createServer(deps, indexUrls, returnMode)
       const transport: StreamableHTTPServerTransport = new StreamableHTTPServerTransport({
         sessionIdGenerator: undefined,
       })
@@ -211,10 +230,10 @@ function createStatelessHttpServer(deps: string[], returnMode: string): http.Ser
   })
 }
 
-function createStatefulHttpServer(deps: string[], returnMode: string): http.Server {
+function createStatefulHttpServer(deps: string[], indexUrls: string[], returnMode: string): http.Server {
   // Stateful mode with session management
   // https://github.com/modelcontextprotocol/typescript-sdk?tab=readme-ov-file#with-session-management
-  const mcpServer = createServer(deps, returnMode)
+  const mcpServer = createServer(deps, indexUrls, returnMode)
   const transports: { [sessionId: string]: StreamableHTTPServerTransport } = {}
 
   return http.createServer(async (req, res) => {
@@ -293,8 +312,8 @@ function createStatefulHttpServer(deps: string[], returnMode: string): http.Serv
 /*
  * Run the MCP server using the Stdio transport.
  */
-async function runStdio(deps: string[], returnMode: string) {
-  const mcpServer = createServer(deps, returnMode)
+async function runStdio(deps: string[], indexUrls: string[], returnMode: string) {
+  const mcpServer = createServer(deps, indexUrls, returnMode)
   const transport = new StdioServerTransport()
   await mcpServer.connect(transport)
 }
@@ -302,10 +321,11 @@ async function runStdio(deps: string[], returnMode: string) {
 /*
  * Run pyodide to download and install dependencies.
  */
-async function installDeps(deps: string[]) {
+async function installDeps(deps: string[], indexUrls: string[]) {
   const runCode = new RunCode()
   const result = await runCode.run(
     deps,
+    indexUrls,
     (level, data) => console.error(`${level}|${data}`),
   )
   if (result.status !== 'success') {
@@ -317,7 +337,7 @@ async function installDeps(deps: string[]) {
 /*
  * Run a short example script that requires numpy.
  */
-async function example(deps: string[]) {
+async function example(deps: string[], indexUrls: string[]) {
   console.error(
     `Running example script for MCP Run Python version ${VERSION}...`,
   )
@@ -330,6 +350,7 @@ a
   const runCode = new RunCode()
   const result = await runCode.run(
     deps,
+    indexUrls,
     // use warn to avoid recursion since console.log is patched in runCode
     (level, data) => console.warn(`${level}: ${data}`),
     { name: 'example.py', content: code },
diff --git a/mcp_run_python/deno/src/runCode.ts b/mcp_run_python/deno/src/runCode.ts
index 1be8681..2871cf4 100644
--- a/mcp_run_python/deno/src/runCode.ts
+++ b/mcp_run_python/deno/src/runCode.ts
@@ -23,6 +23,7 @@ export class RunCode {
 
   async run(
     dependencies: string[],
+    indexUrls: string[],
     log: (level: LoggingLevel, data: string) => void,
     file?: CodeFile,
     globals?: Record<string, any>,
@@ -38,7 +39,7 @@ export class RunCode {
       sys = pyodide.pyimport('sys')
     } else {
       if (!this.prepPromise) {
-        this.prepPromise = this.prepEnv(dependencies, log)
+        this.prepPromise = this.prepEnv(dependencies, indexUrls, log)
       }
       // TODO is this safe if the promise has already been accessed? it seems to work fine
       const prep = await this.prepPromise
@@ -83,6 +84,7 @@ export class RunCode {
 
   async prepEnv(
     dependencies: string[],
+    indexUrls: string[],
     log: (level: LoggingLevel, data: string) => void,
   ): Promise<PrepResult> {
     const pyodide = await loadPyodide({
@@ -122,7 +124,10 @@ export class RunCode {
 
     const preparePyEnv: PreparePyEnv = pyodide.pyimport(moduleName)
 
-    const prepareStatus = await preparePyEnv.prepare_env(pyodide.toPy(dependencies))
+    const prepareStatus = await preparePyEnv.prepare_env(
+      pyodide.toPy(dependencies),
+      pyodide.toPy(indexUrls),
+    )
     return {
       pyodide,
       preparePyEnv,
@@ -214,6 +219,6 @@ interface PrepareError {
   message: string
 }
 interface PreparePyEnv {
-  prepare_env: (files: CodeFile[]) => Promise<PrepareSuccess | PrepareError>
+  prepare_env: (dependencies: any, index_urls: any) => Promise<PrepareSuccess | PrepareError>
   dump_json: (value: any, always_return_json: boolean) => string | null
 }
diff --git a/mcp_run_python/main.py b/mcp_run_python/main.py
index 1b95224..5b6e93d 100644
--- a/mcp_run_python/main.py
+++ b/mcp_run_python/main.py
@@ -24,6 +24,7 @@ def run_mcp_server(
     *,
     http_port: int | None = None,
     dependencies: list[str] | None = None,
+    index_urls: list[str] | None = None,
     return_mode: Literal['json', 'xml'] = 'xml',
     deps_log_handler: LogHandler | None = None,
     allow_networking: bool = True,
@@ -35,6 +36,7 @@ def run_mcp_server(
         mode: The mode to run the server in.
         http_port: The port to run the server on if mode is `streamable_http`.
         dependencies: The dependencies to install.
+        index_urls: Package index URLs for installing dependencies (tried in order before PyPI).
         return_mode: The mode to return tool results in.
         deps_log_handler: Optional function to receive logs emitted while installing dependencies.
         allow_networking: Whether to allow networking when running provided python code.
@@ -48,6 +50,7 @@ def run_mcp_server(
     with prepare_deno_env(
         mode,
         dependencies=dependencies,
+        index_urls=index_urls,
         http_port=http_port,
         return_mode=return_mode,
         deps_log_handler=deps_log_handler,
@@ -79,6 +82,7 @@ def prepare_deno_env(
     *,
     http_port: int | None = None,
     dependencies: list[str] | None = None,
+    index_urls: list[str] | None = None,
     return_mode: Literal['json', 'xml'] = 'xml',
     deps_log_handler: LogHandler | None = None,
     allow_networking: bool = True,
@@ -93,6 +97,7 @@ def prepare_deno_env(
         mode: The mode to run the server in.
         http_port: The port to run the server on if mode is `streamable_http`.
         dependencies: The dependencies to install.
+        index_urls: Package index URLs for installing dependencies (tried in order before PyPI).
         return_mode: The mode to return tool results in.
         deps_log_handler: Optional function to receive logs emitted while installing dependencies.
         allow_networking: Whether the prepared DenoEnv should allow networking when running code.
@@ -108,7 +113,7 @@ def prepare_deno_env(
         shutil.copytree(src, cwd, ignore=shutil.ignore_patterns('node_modules'))
         logger.info('Installing dependencies %s...', dependencies)
 
-        args = 'deno', *_deno_install_args(dependencies)
+        args = 'deno', *_deno_install_args(dependencies, index_urls)
         p = subprocess.Popen(args, cwd=cwd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
         stdout: list[str] = []
         if p.stdout is not None:
@@ -127,6 +132,7 @@ def prepare_deno_env(
             mode,
             http_port=http_port,
             dependencies=dependencies,
+            index_urls=index_urls,
             return_mode=return_mode,
             allow_networking=allow_networking,
         )
@@ -142,6 +148,7 @@ async def async_prepare_deno_env(
     *,
     http_port: int | None = None,
     dependencies: list[str] | None = None,
+    index_urls: list[str] | None = None,
     return_mode: Literal['json', 'xml'] = 'xml',
     deps_log_handler: LogHandler | None = None,
     allow_networking: bool = True,
@@ -152,6 +159,7 @@ async def async_prepare_deno_env(
         mode,
         http_port=http_port,
         dependencies=dependencies,
+        index_urls=index_urls,
         return_mode=return_mode,
         deps_log_handler=deps_log_handler,
         allow_networking=allow_networking,
@@ -162,7 +170,7 @@ async def async_prepare_deno_env(
         await _asyncify(ct.__exit__, None, None, None)
 
 
-def _deno_install_args(dependencies: list[str] | None = None) -> list[str]:
+def _deno_install_args(dependencies: list[str] | None = None, index_urls: list[str] | None = None) -> list[str]:
     args = [
         'run',
         '--allow-net',
@@ -173,7 +181,11 @@ def _deno_install_args(dependencies: list[str] | None = None) -> list[str]:
         'noop',
     ]
     if dependencies is not None:
-        args.append(f'--deps={",".join(dependencies)}')
+        for dep in dependencies:
+            args.append(f'--dep={dep}')
+    if index_urls:
+        for url in index_urls:
+            args.append(f'--index-url={url}')
     return args
 
 
@@ -182,6 +194,7 @@ def _deno_run_args(
     *,
     http_port: int | None = None,
     dependencies: list[str] | None = None,
+    index_urls: list[str] | None = None,
     return_mode: Literal['json', 'xml'] = 'xml',
     allow_networking: bool = True,
 ) -> list[str]:
@@ -196,7 +209,11 @@ def _deno_run_args(
         f'--return-mode={return_mode}',
     ]
     if dependencies is not None:
-        args.append(f'--deps={",".join(dependencies)}')
+        for dep in dependencies:
+            args.append(f'--dep={dep}')
+    if index_urls:
+        for url in index_urls:
+            args.append(f'--index-url={url}')
     if http_port is not None:
         if mode in ('streamable_http', 'streamable_http_stateless'):
             args.append(f'--port={http_port}')
diff --git a/tests/test_cli.py b/tests/test_cli.py
index b86bd4c..170f94b 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -1,5 +1,7 @@
 from __future__ import annotations as _annotations
 
+import warnings
+
 import pytest
 
 from mcp_run_python._cli import cli_logic
@@ -15,5 +17,30 @@ def test_cli_example_success():
     assert cli_logic(['--deps', 'numpy', 'example']) == 0
 
 
+def test_cli_dep_repeatable():
+    """Test new --dep repeatable flag"""
+    assert cli_logic(['--dep', 'numpy', 'example']) == 0
+
+
+def test_cli_dep_multiple():
+    """Test multiple --dep flags"""
+    assert cli_logic(['--dep', 'numpy', '--dep', 'pydantic', 'example']) == 0
+
+
+def test_cli_dep_and_deps_combined():
+    """Test combining --dep and --deps (backwards compat)"""
+    assert cli_logic(['--dep', 'numpy', '--deps', 'pydantic', 'example']) == 0
+
+
+def test_cli_deps_deprecation_warning():
+    """Test that --deps emits a deprecation warning"""
+    with warnings.catch_warnings(record=True) as w:
+        warnings.simplefilter('always')
+        cli_logic(['--deps', 'numpy', 'example'])
+        deprecation_warnings = [x for x in w if issubclass(x.category, DeprecationWarning)]
+        assert len(deprecation_warnings) >= 1
+        assert any('--deps is deprecated' in str(x.message) for x in deprecation_warnings)
+
+
 def test_cli_example_fail():
     assert cli_logic(['example']) == 1