diff --git a/cli/main.rs b/cli/main.rs
index 55f1ac9ce0..0cbf61c61c 100644
--- a/cli/main.rs
+++ b/cli/main.rs
@@ -948,11 +948,31 @@ async fn run_command(flags: Flags, script: String) -> Result<(), AnyError> {
   let permissions = Permissions::from_options(&flags.clone().into());
   let mut worker =
     create_main_worker(&program_state, main_module.clone(), permissions);
+
+  let mut maybe_coverage_collector =
+    if let Some(ref coverage_dir) = program_state.coverage_dir {
+      let session = worker.create_inspector_session();
+
+      let coverage_dir = PathBuf::from(coverage_dir);
+      let mut coverage_collector =
+        tools::coverage::CoverageCollector::new(coverage_dir, session);
+      coverage_collector.start_collecting().await?;
+
+      Some(coverage_collector)
+    } else {
+      None
+    };
+
   debug!("main_module {}", main_module);
   worker.execute_module(&main_module).await?;
   worker.execute("window.dispatchEvent(new Event('load'))")?;
   worker.run_event_loop().await?;
   worker.execute("window.dispatchEvent(new Event('unload'))")?;
+
+  if let Some(coverage_collector) = maybe_coverage_collector.as_mut() {
+    coverage_collector.stop_collecting().await?;
+  }
+
   Ok(())
 }
 
diff --git a/cli/tests/integration_tests.rs b/cli/tests/integration_tests.rs
index 5696f1f5bc..67cafeeca0 100644
--- a/cli/tests/integration_tests.rs
+++ b/cli/tests/integration_tests.rs
@@ -3322,6 +3322,12 @@ itest!(deno_test_run_test_coverage {
   exit_code: 0,
 });
 
+itest!(deno_test_run_run_coverage {
+  args: "test --allow-all --coverage --unstable test_run_run_coverage.ts",
+  output: "test_run_run_coverage.out",
+  exit_code: 0,
+});
+
 itest!(deno_lint {
   args: "lint --unstable lint/file1.js lint/file2.ts lint/ignored_file.ts",
   output: "lint/expected.out",
diff --git a/cli/tests/run_coverage.ts b/cli/tests/run_coverage.ts
new file mode 100644
index 0000000000..098d463e8d
--- /dev/null
+++ b/cli/tests/run_coverage.ts
@@ -0,0 +1,3 @@
+import { returnsFoo2 } from "./subdir/mod1.ts";
+
+returnsFoo2();
diff --git a/cli/tests/test_run_run_coverage.out b/cli/tests/test_run_run_coverage.out
new file mode 100644
index 0000000000..15ea230ef3
--- /dev/null
+++ b/cli/tests/test_run_run_coverage.out
@@ -0,0 +1,27 @@
+Check [WILDCARD]/$deno$test.ts
+running 1 tests
+test spawn test ... Check [WILDCARD]/run_coverage.ts
+ok ([WILDCARD])
+
+test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out ([WILDCARD])
+
+cover [WILDCARD]/tests/run_coverage.ts ... 100.000% (3/3)
+cover [WILDCARD]/tests/subdir/mod1.ts ... 35.714% (5/14)
+   2 | export function returnsHi() {
+   3 |     return "Hi";
+   4 | }
+-----|-----
+   8 | export function printHello3() {
+   9 |     printHello2();
+  10 | }
+  11 | export function throwsError() {
+  12 |     throw Error("exception from mod1");
+  13 | }
+cover [WILDCARD]/tests/subdir/print_hello.ts ... 25.000% (1/4)
+   1 | export function printHello() {
+   2 |     console.log("Hello");
+   3 | }
+cover [WILDCARD]/tests/subdir/subdir2/mod2.ts ... 62.500% (5/8)
+   5 | export function printHello2() {
+   6 |     printHello();
+   7 | }
diff --git a/cli/tests/test_run_run_coverage.ts b/cli/tests/test_run_run_coverage.ts
new file mode 100644
index 0000000000..448b15e7b6
--- /dev/null
+++ b/cli/tests/test_run_run_coverage.ts
@@ -0,0 +1,14 @@
+Deno.test("spawn test", async function () {
+  const process = Deno.run({
+    cmd: [
+      Deno.execPath(),
+      "run",
+      "--allow-all",
+      "--unstable",
+      "run_coverage.ts",
+    ],
+  });
+
+  await process.status();
+  process.close();
+});