diff --git a/CHANGELOG.md b/CHANGELOG.md
index 25e9793b..f91db1e8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- Patching: removing one `[[table]]` entry no longer deletes the sub-tables of the other entries. ([#321])
+
 ## [3.3.0] - 2026-09-27
 
 ### Added
@@ -501,5 +505,6 @@ This first forked version from [timhall/toml-patch](https://github.com/timhall/t
 [#313]: https://github.com/DecimalTurn/toml-patch/pull/313
 [#314]: https://github.com/DecimalTurn/toml-patch/pull/314
 [#316]: https://github.com/DecimalTurn/toml-patch/pull/316
+[#321]: https://github.com/DecimalTurn/toml-patch/pull/321
 [0e66e68]: https://github.com/DecimalTurn/toml-patch/commit/0e66e68cbf42a07bc44445e46c3ea7bea97f95c1
 [f97d571]: https://github.com/DecimalTurn/toml-patch/commit/f97d57194952b6603f0fcd686c32d3ae52a2c903
diff --git a/src/__tests__/patch.test.ts b/src/__tests__/patch.test.ts
index 6a374f67..ecd7a79f 100644
--- a/src/__tests__/patch.test.ts
+++ b/src/__tests__/patch.test.ts
@@ -2098,6 +2098,104 @@ test('should remove table array and preserve leading KV', () => {
   expect(patched).not.toContain('name');
 });
 
+test('should remove one table array entry and keep the sub-tables of the others', () => {
+  const existing = dedent`
+    [[route]]
+    id = "a"
+    [route.args]
+    x = 1
+
+    [[route]]
+    id = "b"
+    [route.args]
+    y = 2
+
+    [[route]]
+    id = "c"
+    [route.args]
+    z = 3
+  ` + '\n';
+
+  for (const removed of [0, 1, 2]) {
+    const updated = parse(existing) as { route: object[] };
+    updated.route.splice(removed, 1);
+
+    const patched = patch(existing, updated);
+    const expected = [
+      dedent`
+        [[route]]
+        id = "b"
+        [route.args]
+        y = 2
+
+        [[route]]
+        id = "c"
+        [route.args]
+        z = 3
+      ` + '\n',
+      dedent`
+        [[route]]
+        id = "a"
+        [route.args]
+        x = 1
+
+        [[route]]
+        id = "c"
+        [route.args]
+        z = 3
+      ` + '\n',
+      dedent`
+        [[route]]
+        id = "a"
+        [route.args]
+        x = 1
+
+        [[route]]
+        id = "b"
+        [route.args]
+        y = 2
+      ` + '\n',
+    ];
+
+    expect(patched).toBe(expected[removed]);
+    expect(parse(patched)).toEqual(updated);
+  }
+});
+
+test('should remove a nested table array entry and keep the next parent entry\'s sub-tables', () => {
+  const existing = dedent`
+    [[group]]
+    id = "g0"
+    [[group.route]]
+    id = "a"
+    [[group.route]]
+    id = "b"
+
+    [[group]]
+    id = "g1"
+    [group.route.args]
+    x = 1
+  ` + '\n';
+
+  const updated = parse(existing) as { group: { route: object[] }[] };
+  updated.group[0].route.splice(1, 1);
+  const patched = patch(existing, updated);
+  const expected = dedent`
+    [[group]]
+    id = "g0"
+    [[group.route]]
+    id = "a"
+
+    [[group]]
+    id = "g1"
+    [group.route.args]
+    x = 1
+  ` + '\n';
+
+  expect(patched).toBe(expected);
+  expect(parse(patched)).toEqual(updated);
+});
+
 test('should remove leading KV and preserve table array', () => {
   const existing = dedent`
     title = "Project"
diff --git a/src/patch.ts b/src/patch.ts
index 2faf1dfb..08ef6812 100644
--- a/src/patch.ts
+++ b/src/patch.ts
@@ -3200,8 +3200,26 @@ function applyChanges(
           const key = (node as Table | TableArray).key.item.value;
           const siblings = (parent as { items: TreeNode[] }).items;
           const extending: TreeNode[] = [];
-          for (const sibling of siblings) {
+          // A sub-table belongs to the nearest [[x]] entry above it, so an
+          // entry owns only the siblings up to the next entry of its own
+          // array or of an ancestor array ([[x]] ends an [[x.y]] entry too).
+          const aotEntry = isTableArray(node);
+          const ownStart = siblings.indexOf(node);
+          let ownEnd = siblings.length;
+          if (aotEntry) {
+            for (let i = ownStart + 1; i < siblings.length; i++) {
+              const s = siblings[i];
+              if (!isTableArray(s)) continue;
+              const sKey = s.key.item.value;
+              if (sKey.length <= key.length && arraysEqual(sKey, key.slice(0, sKey.length))) {
+                ownEnd = i;
+                break;
+              }
+            }
+          }
+          for (const [index, sibling] of siblings.entries()) {
             if (sibling === node) continue;
+            if (aotEntry && (index < ownStart || index >= ownEnd)) continue;
             const siblingKey = isKeyValue(sibling)
               ? sibling.key.value
               : isTable(sibling) || isTableArray(sibling)