diff --git a/javascript/ql/lib/change-notes/2025-08-01-cli-code-injection.md b/javascript/ql/lib/change-notes/2025-08-01-cli-code-injection.md
new file mode 100644
index 000000000000..20fa14da66f9
--- /dev/null
+++ b/javascript/ql/lib/change-notes/2025-08-01-cli-code-injection.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* Improved modeling of command-line argument parsing libraries [arg](https://www.npmjs.com/package/arg), [args](https://www.npmjs.com/package/args), [command-line-args](https://www.npmjs.com/package/command-line-args) and [commander](https://www.npmjs.com/package/commander)
diff --git a/javascript/ql/lib/semmle/javascript/frameworks/CommandLineArguments.qll b/javascript/ql/lib/semmle/javascript/frameworks/CommandLineArguments.qll
index 50beb04b8879..cd8fa34a08eb 100644
--- a/javascript/ql/lib/semmle/javascript/frameworks/CommandLineArguments.qll
+++ b/javascript/ql/lib/semmle/javascript/frameworks/CommandLineArguments.qll
@@ -87,11 +87,43 @@ private class ArgsParseStep extends TaintTracking::SharedTaintStep {
   override predicate step(DataFlow::Node pred, DataFlow::Node succ) {
     exists(DataFlow::CallNode call |
       call = DataFlow::moduleMember("args", "parse").getACall() or
-      call = DataFlow::moduleImport(["yargs-parser", "minimist", "subarg"]).getACall()
+      call =
+        DataFlow::moduleImport(["yargs-parser", "minimist", "subarg", "yargs/yargs", "yargs"])
+            .getACall()
     |
       succ = call and
       pred = call.getArgument(0)
     )
+    or
+    exists(API::Node commanderNode | commanderNode = commander() |
+      pred = commanderNode.getMember(["parse", "parseAsync"]).getACall().getAnArgument() and
+      succ =
+        [
+          commanderNode.getMember("opts").getACall(), commanderNode.getAMember().asSource(),
+          commander()
+              .getMember("action")
+              .getACall()
+              .getArgument(0)
+              .(DataFlow::FunctionNode)
+              .getAParameter()
+        ]
+    )
+    or
+    exists(DataFlow::MethodCallNode methodCall | methodCall = yargs() |
+      pred = methodCall.getReceiver() and
+      succ = methodCall
+    )
+    or
+    exists(DataFlow::CallNode call, DataFlow::Node options |
+      call = DataFlow::moduleImport(["arg", "command-line-args"]).getACall() and
+      succ = call and
+      options = call.getArgument(1) and
+      exists(DataFlow::PropWrite write |
+        write.getBase() = options and
+        write.getPropertyName() = "argv" and
+        pred = write.getRhs()
+      )
+    )
   }
 }
 
@@ -115,7 +147,9 @@ private API::Node commander() {
  * Either directly imported as a module, or through some chained method call.
  */
 private DataFlow::SourceNode yargs() {
-  result = DataFlow::moduleImport("yargs")
+  result = DataFlow::moduleImport(["yargs", "yargs/yargs"])
+  or
+  result = DataFlow::moduleImport(["yargs", "yargs/yargs"]).getACall()
   or
   // script used to generate list of chained methods: https://gist.github.com/erik-krogh/f8afe952c0577f4b563a993e613269ba
   exists(string method |
diff --git a/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/CommandInjection.expected b/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/CommandInjection.expected
index 22394ec4cb89..862255f70f23 100644
--- a/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/CommandInjection.expected
+++ b/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/CommandInjection.expected
@@ -21,6 +21,12 @@
 | child_process-test.js:75:29:75:31 | cmd | child_process-test.js:73:25:73:31 | req.url | child_process-test.js:75:29:75:31 | cmd | This command line depends on a $@. | child_process-test.js:73:25:73:31 | req.url | user-provided value |
 | child_process-test.js:83:19:83:36 | req.query.fileName | child_process-test.js:83:19:83:36 | req.query.fileName | child_process-test.js:83:19:83:36 | req.query.fileName | This command line depends on a $@. | child_process-test.js:83:19:83:36 | req.query.fileName | user-provided value |
 | child_process-test.js:94:11:94:35 | "ping " ... ms.host | child_process-test.js:94:21:94:30 | ctx.params | child_process-test.js:94:11:94:35 | "ping " ... ms.host | This command line depends on a $@. | child_process-test.js:94:21:94:30 | ctx.params | user-provided value |
+| command-line-libs.js:14:8:14:18 | options.cmd | command-line-libs.js:9:16:9:23 | req.body | command-line-libs.js:14:8:14:18 | options.cmd | This command line depends on a $@. | command-line-libs.js:9:16:9:23 | req.body | user-provided value |
+| command-line-libs.js:15:8:15:18 | program.cmd | command-line-libs.js:9:16:9:23 | req.body | command-line-libs.js:15:8:15:18 | program.cmd | This command line depends on a $@. | command-line-libs.js:9:16:9:23 | req.body | user-provided value |
+| command-line-libs.js:21:12:21:17 | script | command-line-libs.js:9:16:9:23 | req.body | command-line-libs.js:21:12:21:17 | script | This command line depends on a $@. | command-line-libs.js:9:16:9:23 | req.body | user-provided value |
+| command-line-libs.js:29:10:29:24 | parsed['--cmd'] | command-line-libs.js:27:23:27:30 | req.body | command-line-libs.js:29:10:29:24 | parsed['--cmd'] | This command line depends on a $@. | command-line-libs.js:27:23:27:30 | req.body | user-provided value |
+| command-line-libs.js:37:8:37:18 | options.cmd | command-line-libs.js:35:62:35:69 | req.body | command-line-libs.js:37:8:37:18 | options.cmd | This command line depends on a $@. | command-line-libs.js:35:62:35:69 | req.body | user-provided value |
+| command-line-libs.js:49:8:49:17 | parsed.cmd | command-line-libs.js:42:16:42:23 | req.body | command-line-libs.js:49:8:49:17 | parsed.cmd | This command line depends on a $@. | command-line-libs.js:42:16:42:23 | req.body | user-provided value |
 | exec-sh2.js:10:12:10:57 | cp.spaw ... ptions) | exec-sh2.js:14:25:14:31 | req.url | exec-sh2.js:10:40:10:46 | command | This command line depends on a $@. | exec-sh2.js:14:25:14:31 | req.url | user-provided value |
 | exec-sh.js:15:12:15:61 | cp.spaw ... ptions) | exec-sh.js:19:25:19:31 | req.url | exec-sh.js:15:44:15:50 | command | This command line depends on a $@. | exec-sh.js:19:25:19:31 | req.url | user-provided value |
 | execSeries.js:14:41:14:47 | command | execSeries.js:18:34:18:40 | req.url | execSeries.js:14:41:14:47 | command | This command line depends on a $@. | execSeries.js:18:34:18:40 | req.url | user-provided value |
@@ -116,6 +122,35 @@ edges
 | child_process-test.js:73:15:73:38 | url.par ... , true) | child_process-test.js:73:9:73:49 | cmd | provenance |  |
 | child_process-test.js:73:25:73:31 | req.url | child_process-test.js:73:15:73:38 | url.par ... , true) | provenance |  |
 | child_process-test.js:94:21:94:30 | ctx.params | child_process-test.js:94:11:94:35 | "ping " ... ms.host | provenance |  |
+| command-line-libs.js:9:9:9:34 | args | command-line-libs.js:12:17:12:20 | args | provenance |  |
+| command-line-libs.js:9:9:9:34 | args | command-line-libs.js:23:29:23:32 | args | provenance |  |
+| command-line-libs.js:9:16:9:23 | req.body | command-line-libs.js:9:9:9:34 | args | provenance |  |
+| command-line-libs.js:12:17:12:20 | args | command-line-libs.js:13:19:13:32 | program.opts() | provenance |  |
+| command-line-libs.js:12:17:12:20 | args | command-line-libs.js:15:8:15:18 | program.cmd | provenance |  |
+| command-line-libs.js:12:17:12:20 | args | command-line-libs.js:20:14:20:19 | script | provenance |  |
+| command-line-libs.js:13:9:13:32 | options | command-line-libs.js:14:8:14:14 | options | provenance |  |
+| command-line-libs.js:13:19:13:32 | program.opts() | command-line-libs.js:13:9:13:32 | options | provenance |  |
+| command-line-libs.js:14:8:14:14 | options | command-line-libs.js:14:8:14:18 | options.cmd | provenance |  |
+| command-line-libs.js:20:14:20:19 | script | command-line-libs.js:21:12:21:17 | script | provenance |  |
+| command-line-libs.js:23:29:23:32 | args | command-line-libs.js:20:14:20:19 | script | provenance |  |
+| command-line-libs.js:27:11:27:41 | argsArray | command-line-libs.js:28:53:28:61 | argsArray | provenance |  |
+| command-line-libs.js:27:23:27:30 | req.body | command-line-libs.js:27:11:27:41 | argsArray | provenance |  |
+| command-line-libs.js:28:11:28:64 | parsed | command-line-libs.js:29:10:29:15 | parsed | provenance |  |
+| command-line-libs.js:28:20:28:64 | arg({ ' ... rray }) | command-line-libs.js:28:11:28:64 | parsed | provenance |  |
+| command-line-libs.js:28:53:28:61 | argsArray | command-line-libs.js:28:20:28:64 | arg({ ' ... rray }) | provenance |  |
+| command-line-libs.js:29:10:29:15 | parsed | command-line-libs.js:29:10:29:24 | parsed['--cmd'] | provenance |  |
+| command-line-libs.js:35:9:35:83 | options | command-line-libs.js:37:8:37:14 | options | provenance |  |
+| command-line-libs.js:35:19:35:83 | command ... \| [] }) | command-line-libs.js:35:9:35:83 | options | provenance |  |
+| command-line-libs.js:35:62:35:69 | req.body | command-line-libs.js:35:19:35:83 | command ... \| [] }) | provenance |  |
+| command-line-libs.js:37:8:37:14 | options | command-line-libs.js:37:8:37:18 | options.cmd | provenance |  |
+| command-line-libs.js:42:9:42:34 | args | command-line-libs.js:43:24:43:27 | args | provenance |  |
+| command-line-libs.js:42:16:42:23 | req.body | command-line-libs.js:42:9:42:34 | args | provenance |  |
+| command-line-libs.js:43:9:47:12 | parsed | command-line-libs.js:49:8:49:13 | parsed | provenance |  |
+| command-line-libs.js:43:18:43:28 | yargs(args) | command-line-libs.js:43:18:47:4 | yargs(a ... ue\\n  }) | provenance |  |
+| command-line-libs.js:43:18:47:4 | yargs(a ... ue\\n  }) | command-line-libs.js:43:18:47:12 | yargs(a ... parse() | provenance |  |
+| command-line-libs.js:43:18:47:12 | yargs(a ... parse() | command-line-libs.js:43:9:47:12 | parsed | provenance |  |
+| command-line-libs.js:43:24:43:27 | args | command-line-libs.js:43:18:43:28 | yargs(args) | provenance |  |
+| command-line-libs.js:49:8:49:13 | parsed | command-line-libs.js:49:8:49:17 | parsed.cmd | provenance |  |
 | exec-sh2.js:9:17:9:23 | command | exec-sh2.js:10:40:10:46 | command | provenance |  |
 | exec-sh2.js:14:9:14:49 | cmd | exec-sh2.js:15:12:15:14 | cmd | provenance |  |
 | exec-sh2.js:14:15:14:38 | url.par ... , true) | exec-sh2.js:14:9:14:49 | cmd | provenance |  |
@@ -269,6 +304,38 @@ nodes
 | child_process-test.js:83:19:83:36 | req.query.fileName | semmle.label | req.query.fileName |
 | child_process-test.js:94:11:94:35 | "ping " ... ms.host | semmle.label | "ping " ... ms.host |
 | child_process-test.js:94:21:94:30 | ctx.params | semmle.label | ctx.params |
+| command-line-libs.js:9:9:9:34 | args | semmle.label | args |
+| command-line-libs.js:9:16:9:23 | req.body | semmle.label | req.body |
+| command-line-libs.js:12:17:12:20 | args | semmle.label | args |
+| command-line-libs.js:13:9:13:32 | options | semmle.label | options |
+| command-line-libs.js:13:19:13:32 | program.opts() | semmle.label | program.opts() |
+| command-line-libs.js:14:8:14:14 | options | semmle.label | options |
+| command-line-libs.js:14:8:14:18 | options.cmd | semmle.label | options.cmd |
+| command-line-libs.js:15:8:15:18 | program.cmd | semmle.label | program.cmd |
+| command-line-libs.js:20:14:20:19 | script | semmle.label | script |
+| command-line-libs.js:21:12:21:17 | script | semmle.label | script |
+| command-line-libs.js:23:29:23:32 | args | semmle.label | args |
+| command-line-libs.js:27:11:27:41 | argsArray | semmle.label | argsArray |
+| command-line-libs.js:27:23:27:30 | req.body | semmle.label | req.body |
+| command-line-libs.js:28:11:28:64 | parsed | semmle.label | parsed |
+| command-line-libs.js:28:20:28:64 | arg({ ' ... rray }) | semmle.label | arg({ ' ... rray }) |
+| command-line-libs.js:28:53:28:61 | argsArray | semmle.label | argsArray |
+| command-line-libs.js:29:10:29:15 | parsed | semmle.label | parsed |
+| command-line-libs.js:29:10:29:24 | parsed['--cmd'] | semmle.label | parsed['--cmd'] |
+| command-line-libs.js:35:9:35:83 | options | semmle.label | options |
+| command-line-libs.js:35:19:35:83 | command ... \| [] }) | semmle.label | command ... \| [] }) |
+| command-line-libs.js:35:62:35:69 | req.body | semmle.label | req.body |
+| command-line-libs.js:37:8:37:14 | options | semmle.label | options |
+| command-line-libs.js:37:8:37:18 | options.cmd | semmle.label | options.cmd |
+| command-line-libs.js:42:9:42:34 | args | semmle.label | args |
+| command-line-libs.js:42:16:42:23 | req.body | semmle.label | req.body |
+| command-line-libs.js:43:9:47:12 | parsed | semmle.label | parsed |
+| command-line-libs.js:43:18:43:28 | yargs(args) | semmle.label | yargs(args) |
+| command-line-libs.js:43:18:47:4 | yargs(a ... ue\\n  }) | semmle.label | yargs(a ... ue\\n  }) |
+| command-line-libs.js:43:18:47:12 | yargs(a ... parse() | semmle.label | yargs(a ... parse() |
+| command-line-libs.js:43:24:43:27 | args | semmle.label | args |
+| command-line-libs.js:49:8:49:13 | parsed | semmle.label | parsed |
+| command-line-libs.js:49:8:49:17 | parsed.cmd | semmle.label | parsed.cmd |
 | exec-sh2.js:9:17:9:23 | command | semmle.label | command |
 | exec-sh2.js:10:40:10:46 | command | semmle.label | command |
 | exec-sh2.js:14:9:14:49 | cmd | semmle.label | cmd |
diff --git a/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/command-line-libs.js b/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/command-line-libs.js
new file mode 100644
index 000000000000..83c824d4239a
--- /dev/null
+++ b/javascript/ql/test/query-tests/Security/CWE-078/CommandInjection/command-line-libs.js
@@ -0,0 +1,50 @@
+import express from 'express';
+import { Command } from 'commander';
+import { exec } from 'child_process';
+import arg from 'arg';
+const app = express();
+app.use(express.json());
+
+app.post('/Command', async (req, res) => {
+  const args = req.body.args || []; // $ Source
+  const program = new Command();
+  program.option('--cmd <value>', 'Command to execute');
+  program.parse(args, { from: 'user' });
+  const options = program.opts();
+  exec(options.cmd); // $ Alert
+  exec(program.cmd); // $ Alert
+
+  const program1 = new Command();
+  program1
+    .command('run <script>')
+    .action((script) => {
+      exec(script); // $ Alert
+    });
+  await program1.parseAsync(args);
+});
+
+app.post('/arg', (req, res) => {
+    const argsArray = req.body.args || []; // $ Source
+    const parsed = arg({ '--cmd': String }, { argv: argsArray });
+    exec(parsed['--cmd']); // $ Alert
+});
+
+app.post('/commandLineArgs', (req, res) => {
+  const commandLineArgs = require('command-line-args');
+  const optionDefinitions = [{ name: 'cmd', type: String }];
+  const options = commandLineArgs(optionDefinitions, { argv: req.body.args || [] }); // $ Source
+  if (!options.cmd) return res.status(400).send({ error: 'Missing --cmd' });
+  exec(options.cmd); // $ Alert
+});
+
+app.post('/yargs', (req, res) => {
+  const yargs = require('yargs/yargs');
+  const args = req.body.args || []; // $ Source
+  const parsed = yargs(args).option('cmd', {
+    type: 'string',
+    describe: 'Command to execute',
+    demandOption: true
+  }).parse();
+
+  exec(parsed.cmd); // $ Alert
+});