diff --git a/lib/internal/watch_mode/files_watcher.js b/lib/internal/watch_mode/files_watcher.js
index f917a3767e3235..112f0b8be53c50 100644
--- a/lib/internal/watch_mode/files_watcher.js
+++ b/lib/internal/watch_mode/files_watcher.js
@@ -180,7 +180,10 @@ class FilesWatcher extends EventEmitter {
     owners.forEach((owner) => {
       this.#ownerDependencies.get(owner)?.forEach((dependency) => {
         this.#filteredFiles.delete(dependency);
-        this.#dependencyOwners.delete(dependency);
+        this.#dependencyOwners.get(dependency)?.delete(owner);
+        if (this.#dependencyOwners.get(dependency)?.size === 0) {
+          this.#dependencyOwners.delete(dependency);
+        }
       });
       this.#filteredFiles.delete(owner);
       this.#dependencyOwners.delete(owner);
diff --git a/test/parallel/test-runner-complex-dependencies.mjs b/test/parallel/test-runner-complex-dependencies.mjs
new file mode 100644
index 00000000000000..e8aa9630d12af0
--- /dev/null
+++ b/test/parallel/test-runner-complex-dependencies.mjs
@@ -0,0 +1,126 @@
+// Flags: --expose-internals
+import * as common from '../common/index.mjs';
+import { describe, it } from 'node:test';
+import assert from 'node:assert';
+import { spawn } from 'node:child_process';
+import { writeFileSync } from 'node:fs';
+import tmpdir from '../common/tmpdir.js';
+
+if (common.isIBMi)
+  common.skip('IBMi does not support `fs.watch()`');
+
+if (common.isAIX)
+  common.skip('folder watch capability is limited in AIX.');
+
+tmpdir.refresh();
+
+// Set up test files and dependencies
+const fixtureContent = {
+  'dependency.js': 'module.exports = {};',
+  'test.js': `
+const test = require('node:test');
+require('./dependency.js');
+test('first test has ran');`,
+  'test-2.js': `
+const test = require('node:test');
+require('./dependency.js');
+test('second test has ran');`,
+};
+
+const fixturePaths = Object.fromEntries(Object.keys(fixtureContent)
+  .map((file) => [file, tmpdir.resolve(file)]));
+
+Object.entries(fixtureContent)
+  .forEach(([file, content]) => writeFileSync(fixturePaths[file], content));
+
+describe('test runner watch mode with more complex setup', () => {
+  it('should re-run appropriate tests when dependencies change', async () => {
+    // Start the test runner in watch mode
+    const child = spawn(process.execPath,
+                        ['--watch', '--test'],
+                        { encoding: 'utf8', stdio: 'pipe', cwd: tmpdir.path });
+
+    let currentRunOutput = '';
+    const testRuns = [];
+
+    const firstRunCompleted = Promise.withResolvers();
+    const secondRunCompleted = Promise.withResolvers();
+    const thirdRunCompleted = Promise.withResolvers();
+    const fourthRunCompleted = Promise.withResolvers();
+
+    child.stdout.on('data', (data) => {
+      const str = data.toString();
+      currentRunOutput += str;
+
+      if (/duration_ms\s\d+/.test(str)) {
+        // Test run has completed
+        testRuns.push(currentRunOutput);
+        currentRunOutput = '';
+        switch (testRuns.length) {
+          case 1:
+            firstRunCompleted.resolve();
+            break;
+          case 2:
+            secondRunCompleted.resolve();
+            break;
+          case 3:
+            thirdRunCompleted.resolve();
+            break;
+          case 4:
+            fourthRunCompleted.resolve();
+            break;
+        }
+      }
+    });
+
+    // Wait for the initial test run to complete
+    await firstRunCompleted.promise;
+
+    // Modify 'dependency.js' to trigger re-run of both tests
+    writeFileSync(fixturePaths['dependency.js'], 'module.exports = { modified: true };');
+
+    // Wait for the second test run to complete
+    await secondRunCompleted.promise;
+
+    // Modify 'test.js' to trigger re-run of only 'test.js'
+    writeFileSync(fixturePaths['test.js'], `
+const test = require('node:test');
+require('./dependency.js');
+test('first test has ran again');`);
+
+    // Wait for the third test run to complete
+    await thirdRunCompleted.promise;
+
+    // Modify 'dependency.js' again to trigger re-run of both tests
+    writeFileSync(fixturePaths['dependency.js'], 'module.exports = { modified: true, again: true };');
+
+    // Wait for the fourth test run to complete
+    await fourthRunCompleted.promise;
+
+    // Kill the child process
+    child.kill();
+
+    // Analyze the test runs
+    assert.strictEqual(testRuns.length, 4);
+
+    // First test run - Both tests should run
+    const firstRunOutput = testRuns[0];
+    assert.match(firstRunOutput, /first test has ran/);
+    assert.match(firstRunOutput, /second test has ran/);
+
+    // Second test run - We have modified 'dependency.js' only, so both tests should re-run
+    const secondRunOutput = testRuns[1];
+    assert.match(secondRunOutput, /first test has ran/);
+    assert.match(secondRunOutput, /second test has ran/);
+
+    // Third test run - We have modified 'test.js' only
+    const thirdRunOutput = testRuns[2];
+    assert.match(thirdRunOutput, /first test has ran again/);
+    assert.doesNotMatch(thirdRunOutput, /second test has ran/);
+
+    // Fourth test run - We have modified 'dependency.js' again, so both tests should re-run
+    const fourthRunOutput = testRuns[3];
+    assert.match(fourthRunOutput, /first test has ran again/);
+    assert.match(fourthRunOutput, /second test has ran/);
+  });
+});
diff --git a/test/parallel/test-watch-file-shared-dependency.mjs b/test/parallel/test-watch-file-shared-dependency.mjs
new file mode 100644
index 00000000000000..37ac647f82310e
--- /dev/null
+++ b/test/parallel/test-watch-file-shared-dependency.mjs
@@ -0,0 +1,54 @@
+// Flags: --expose-internals
+import * as common from '../common/index.mjs';
+import { describe, it } from 'node:test';
+import assert from 'node:assert';
+import tmpdir from '../common/tmpdir.js';
+import watcher from 'internal/watch_mode/files_watcher';
+import { writeFileSync } from 'node:fs';
+
+if (common.isIBMi)
+  common.skip('IBMi does not support `fs.watch()`');
+
+if (common.isAIX)
+  common.skip('folder watch capability is limited in AIX.');
+
+tmpdir.refresh();
+
+const { FilesWatcher } = watcher;
+
+tmpdir.refresh();
+
+// Set up test files and dependencies
+const fixtureContent = {
+  'dependency.js': 'module.exports = {};',
+  'test.js': 'require(\'./dependency.js\');',
+  'test-2.js': 'require(\'./dependency.js\');',
+};
+
+const fixturePaths = Object.fromEntries(Object.keys(fixtureContent)
+  .map((file) => [file, tmpdir.resolve(file)]));
+
+Object.entries(fixtureContent)
+  .forEach(([file, content]) => writeFileSync(fixturePaths[file], content));
+
+describe('watch file with shared dependency', () => {
+  it('should not remove shared dependencies when unfiltering an owner', () => {
+    const controller = new AbortController();
+    const watcher = new FilesWatcher({ signal: controller.signal, debounce: 200 });
+
+    watcher.on('changed', ({ owners }) => {
+      assert.strictEqual(owners.size, 2);
+      assert.ok(owners.has(fixturePaths['test.js']));
+      assert.ok(owners.has(fixturePaths['test-2.js']));
+      controller.abort();
+    });
+    watcher.filterFile(fixturePaths['test.js']);
+    watcher.filterFile(fixturePaths['test-2.js']);
+    watcher.filterFile(fixturePaths['dependency.js'], fixturePaths['test.js']);
+    watcher.filterFile(fixturePaths['dependency.js'], fixturePaths['test-2.js']);
+    watcher.unfilterFilesOwnedBy([fixturePaths['test.js']]);
+    watcher.filterFile(fixturePaths['test.js']);
+    watcher.filterFile(fixturePaths['dependency.js'], fixturePaths['test.js']);
+    writeFileSync(fixturePaths['dependency.js'], 'module.exports = { modified: true };');
+  });
+});