diff --git a/CHANGELOG.md b/CHANGELOG.md
index b213c935..6abbd044 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 ### Fixed
 
+- Emptying an array of tables under a table that a later header declares (e.g. `[[a.b.c]]` before `[a]` or `[a.b]`), or that a header in an earlier fragment of an out-of-order table declares (e.g. `[a.b]` before `[a]` and `[[a.b.c]]`), no longer renders invalid TOML; the `key = []` fallback is now written under that header. ([#690](https://github.com/python-poetry/tomlkit/issues/690))
 - Arithmetic and `replace()` results for `Integer`, `Float`, `String`, `DateTime`, `Date` and `Time` no longer share the original item's `Trivia`, so changing the result's comment or indentation no longer rewrites the item still stored in the document.
 
 ## [0.15.2] - 2026-10-16
diff --git a/tests/test_toml_document.py b/tests/test_toml_document.py
index 84b114b9..49481fa5 100644
--- a/tests/test_toml_document.py
+++ b/tests/test_toml_document.py
@@ -1,6 +1,7 @@
 import copy
 import json
 import pickle
+import sys
 
 from collections.abc import Callable
 from datetime import datetime
@@ -1804,3 +1805,83 @@ def test_emptied_array_of_tables_is_relative_to_the_nearest_header() -> None:
     doc["t"]["u"]["a"].pop()
 
     assert doc.as_string() == "[t]\nu.a = []\n"
+
+
+@pytest.mark.parametrize(
+    "content",
+    [
+        # The super table is declared later by a header.
+        "[[a.b.c]]\nx = 1\n\n[a]\ny = 1\n",
+        # ... which extends the implicit parent with a dotted key.
+        "[[a.b.c]]\nx = 1\n[a]\nb.z = 1\n",
+        # The implicit parent is declared later by a header.
+        "[[a.b.c]]\nx = 1\n[a.b]\ny = 1\n",
+        # Both are declared later.
+        "[[a.b.c]]\nx = 1\n[a]\ny = 1\n[a.b]\nw = 1\n",
+        # A sibling table header comes before the super table.
+        "[[a.b.c]]\nx = 1\n[a.b.d]\nz = 1\n[a]\ny = 1\n",
+    ],
+)
+def test_emptied_array_of_tables_before_out_of_order_header(content) -> None:
+    # https://github.com/python-poetry/tomlkit/issues/690
+    # The fallback belongs to the header that declares its parent, even when
+    # that header is in a later fragment. Writing `a.b.c = []` at the top
+    # declared `a` before `[a]` did.
+    doc = parse(content)
+    doc["a"]["b"]["c"].pop()
+    out = doc.as_string()
+
+    assert parse(out).unwrap() == doc.unwrap()
+    if sys.version_info >= (3, 11):
+        # tomlkit's own parser accepts some of the broken output.
+        import tomllib
+
+        assert tomllib.loads(out) == doc.unwrap()
+
+
+def test_emptied_array_of_tables_is_written_under_the_out_of_order_header() -> None:
+    doc = parse("[[a.b.c]]\nx = 1\n\n[a]\ny = 1\n")
+    doc["a"]["b"]["c"].pop()
+
+    assert doc.as_string() == "[a]\nb.c = []\ny = 1\n"
+
+
+@pytest.mark.parametrize(
+    "content, path",
+    [
+        # The parent is declared by a header in an earlier fragment of `a`.
+        ("[a.b]\nz = 1\n[a]\ny = 1\n[[a.b.c]]\nx = 1\n", ["a", "b", "c"]),
+        # ... a level deeper, under a super table in both fragments.
+        ("[a.b.d]\nz = 1\n[a]\ny = 1\n[[a.b.d.e]]\nx = 1\n", ["a", "b", "d", "e"]),
+        # ... with a header in between in the later fragment.
+        (
+            "[a.b.d]\nz = 1\n[a]\ny = 1\n[a.b]\nw = 1\n[[a.b.d.e]]\nx = 1\n",
+            ["a", "b", "d", "e"],
+        ),
+    ],
+)
+def test_emptied_array_of_tables_after_out_of_order_header(
+    content: str, path: list[str]
+) -> None:
+    # The header declaring the parent comes first, in another fragment of the
+    # out-of-order table, so the fallback has to be handed to it before it is
+    # rendered.
+    doc = parse(content)
+    aot: Any = doc
+    for key in path:
+        aot = aot[key]
+    aot.pop()
+    out = doc.as_string()
+
+    assert parse(out).unwrap() == doc.unwrap()
+    if sys.version_info >= (3, 11):
+        import tomllib
+
+        assert tomllib.loads(out) == doc.unwrap()
+
+
+def test_emptied_array_of_tables_is_written_under_the_earlier_fragment() -> None:
+    doc = parse("[a.b]\nz = 1\n[a]\ny = 1\n[[a.b.c]]\nx = 1\n")
+    doc["a"]["b"]["c"].pop()
+
+    assert doc.as_string() == "[a.b]\nc = []\nz = 1\n[a]\ny = 1\n"
diff --git a/tomlkit/container.py b/tomlkit/container.py
index 9265c740..eb6c09ad 100644
--- a/tomlkit/container.py
+++ b/tomlkit/container.py
@@ -3,6 +3,7 @@
 import copy
 import math
 
+from collections import Counter
 from collections.abc import Iterator
 from typing import TYPE_CHECKING
 from typing import Any
@@ -64,8 +65,8 @@ def _emits_header(key: Key, table: Table) -> bool:
 
 
 def _header_less_aots(
-    body: list[tuple[Key | None, Item]], prefix: str = ""
-) -> list[tuple[str, AoT]]:
+    body: list[tuple[Key | None, Item]], prefix: tuple[Key, ...] = ()
+) -> list[tuple[tuple[Key, ...], AoT]]:
     """Every emptied array of tables reachable without crossing a header.
 
     An emptied array of tables has no ``[[key]]`` header left to render, so it
@@ -75,14 +76,14 @@ def _header_less_aots(
     with a key relative to it, and that includes the ones sitting inside super
     tables, which emit no header to separate them.
 
-    Returns ``(dotted key, aot)`` pairs, keyed relative to the scope ``body``
+    Returns ``(key path, aot)`` pairs, keyed relative to the scope ``body``
     belongs to.
     """
-    found: list[tuple[str, AoT]] = []
+    found: list[tuple[tuple[Key, ...], AoT]] = []
     for k, v in body:
         if k is None:
             continue
-        path = f"{prefix}.{k.as_string()}" if prefix else k.as_string()
+        path = (*prefix, k)
         if _is_empty_aot(v):
             found.append((path, v))
         elif isinstance(v, Table) and not _emits_header(k, v):
@@ -90,6 +91,113 @@ def _header_less_aots(
     return found
 
 
+def _declaring_table(
+    body: list[tuple[Key | None, Item]], path: tuple[Key, ...]
+) -> tuple[Table, tuple[Key, ...]] | None:
+    """The deepest table whose header declares a parent of ``path``.
+
+    An out-of-order table is split into fragments, so that header may be in a
+    different fragment than the array of tables itself. A fallback written
+    with a dotted key above it would declare the table a second time.
+
+    Returns the table and ``path`` relative to it, or ``None`` if no header
+    in ``body`` declares a parent of ``path``.
+    """
+    if len(path) < 2:
+        return None
+    found = None
+    for k, v in body:
+        if k != path[0] or not isinstance(v, Table):
+            continue
+        candidate = _declaring_table(v.value.body, path[1:])
+        if candidate is None and _emits_header(k, v):
+            candidate = (v, path[1:])
+        if candidate is not None and (
+            found is None or len(candidate[1]) < len(found[1])
+        ):
+            found = candidate
+    return found
+
+
+def _fragment_aots(
+    body: list[tuple[Key | None, Item]], prefix: tuple[Key, ...] = ()
+) -> list[tuple[tuple[Key, ...], AoT, Table]]:
+    """Every emptied array of tables under a header of an out-of-order table.
+
+    The header declaring its parent may be in an earlier fragment, which is
+    rendered before the header the array of tables sits under, so only the
+    scope holding all the fragments can hand the fallback over in time.
+
+    Returns ``(key path, aot, table)`` triples, keyed relative to the scope
+    ``body`` belongs to, where ``table`` is the closest header above ``aot``.
+    """
+    found: list[tuple[tuple[Key, ...], AoT, Table]] = []
+    counts = Counter(k for k, _ in body if k is not None)
+    for k, v in body:
+        if k is None or not isinstance(v, Table):
+            continue
+        path = (*prefix, k)
+        if not _emits_header(k, v):
+            found.extend(_fragment_aots(v.value.body, path))
+        elif counts[k] > 1:
+            found.extend(_aots_below(v, path, v))
+    return found
+
+
+def _aots_below(
+    table: Table, prefix: tuple[Key, ...], header: Table
+) -> list[tuple[tuple[Key, ...], AoT, Table]]:
+    """Every emptied array of tables below ``table``, across headers.
+
+    Returns ``(key path, aot, table)`` triples like ``_fragment_aots()``,
+    starting from ``prefix`` and ``header``.
+    """
+    found: list[tuple[tuple[Key, ...], AoT, Table]] = []
+    for k, v in table.value.body:
+        if k is None:
+            continue
+        path = (*prefix, k)
+        if _is_empty_aot(v):
+            found.append((path, v, header))
+        elif isinstance(v, Table):
+            found.extend(_aots_below(v, path, v if _emits_header(k, v) else header))
+    return found
+
+
+def _scope_aots(
+    body: list[tuple[Key | None, Item]],
+    inherited: list[tuple[tuple[Key, ...], AoT]],
+    delegated: dict[int, list[tuple[tuple[Key, ...], AoT]]],
+) -> list[tuple[str, AoT]]:
+    """The fallbacks to write at the top of the scope ``body`` belongs to.
+
+    Those whose parent is declared by a header within the scope are left in
+    ``delegated``, keyed by the ``id()`` of that table, for it to write. One
+    handed to a header in another fragment is also keyed by its own ``id()``,
+    so the scope it sits in does not write it a second time.
+
+    Returns ``(dotted key, aot)`` pairs, keyed relative to the scope.
+    """
+    for path, aot, header in _fragment_aots(body):
+        declaring = _declaring_table(body, path)
+        if id(aot) not in delegated and declaring and declaring[0] is not header:
+            table, rest = declaring
+            delegated.setdefault(id(table), []).append((rest, aot))
+            delegated[id(aot)] = []
+    found: list[tuple[str, AoT]] = []
+    for path, aot in [
+        *inherited,
+        *((p, a) for p, a in _header_less_aots(body) if id(a) not in delegated),
+    ]:
+        declaring = _declaring_table(body, path)
+        if declaring is None:
+            found.append((".".join(k.as_string() for k in path), aot))
+        else:
+            table, rest = declaring
+            delegated.setdefault(id(table), []).append((rest, aot))
+    return found
+
+
 def _render_empty_aot(key: str, aot: AoT) -> str:
     """Render an emptied array of tables as an inline empty array."""
     return (
@@ -709,7 +817,8 @@ def last_item(self) -> Item | None:
     def as_string(self) -> str:
         """Render as TOML string."""
         s = ""
-        for path, aot in _header_less_aots(self._body):
+        delegated: dict[int, list[tuple[tuple[Key, ...], AoT]]] = {}
+        for path, aot in _scope_aots(self._body, [], delegated):
             s += _render_empty_aot(path, aot)
         for k, v in self._body:
             if k is not None:
@@ -722,7 +831,7 @@ def as_string(self) -> str:
                         and "\n" not in v.trivia.indent
                     ):
                         s += "\n"
-                    s += self._render_table(k, v)
+                    s += self._render_table(k, v, delegated=delegated)
                 elif isinstance(v, AoT):
                     if (
                         s.strip(" ")
@@ -738,8 +847,16 @@ def as_string(self) -> str:
 
         return s
 
-    def _render_table(self, key: Key, table: Table, prefix: str | None = None) -> str:
+    def _render_table(
+        self,
+        key: Key,
+        table: Table,
+        prefix: str | None = None,
+        delegated: dict[int, list[tuple[tuple[Key, ...], AoT]]] | None = None,
+    ) -> str:
         cur = ""
+        if delegated is None:
+            delegated = {}
 
         if table.display_name is not None:
             _key = table.display_name
@@ -774,7 +891,8 @@ def _render_table(self, key: Key, table: Table, prefix: str | None = None) -> st
         if header_emitted:
             # A super table opens no scope, so its fallbacks belong to -- and
             # were already written by -- the nearest enclosing header instead.
-            for path, aot in _header_less_aots(table.value.body):
+            inherited = delegated.pop(id(table), [])
+            for path, aot in _scope_aots(table.value.body, inherited, delegated):
                 cur += _render_empty_aot(path, aot)
         for k, v in table.value.body:
             if k is not None and _is_empty_aot(v):
@@ -790,11 +908,13 @@ def _render_table(self, key: Key, table: Table, prefix: str | None = None) -> st
                 if v.is_super_table():
                     if k.is_dotted() and not key.is_dotted():
                         # Dotted key inside table
-                        cur += self._render_table(k, v)
+                        cur += self._render_table(k, v, delegated=delegated)
                     else:
-                        cur += self._render_table(k, v, prefix=_key)
+                        cur += self._render_table(
+                            k, v, prefix=_key, delegated=delegated
+                        )
                 else:
-                    cur += self._render_table(k, v, prefix=_key)
+                    cur += self._render_table(k, v, prefix=_key, delegated=delegated)
             elif isinstance(v, AoT):
                 if (
                     cur.strip(" ")
@@ -838,7 +958,8 @@ def _render_aot_table(self, table: Table, prefix: str | None = None) -> str:
             f"{table.trivia.trail}"
         )
 
-        for path, aot in _header_less_aots(table.value.body):
+        delegated: dict[int, list[tuple[tuple[Key, ...], AoT]]] = {}
+        for path, aot in _scope_aots(table.value.body, [], delegated):
             cur += _render_empty_aot(path, aot)
         for k, v in table.value.body:
             if k is not None and _is_empty_aot(v):
@@ -848,11 +969,13 @@ def _render_aot_table(self, table: Table, prefix: str | None = None) -> str:
                 if v.is_super_table():
                     if k.is_dotted():
                         # Dotted key inside table
-                        cur += self._render_table(k, v)
+                        cur += self._render_table(k, v, delegated=delegated)
                     else:
-                        cur += self._render_table(k, v, prefix=_key)
+                        cur += self._render_table(
+                            k, v, prefix=_key, delegated=delegated
+                        )
                 else:
-                    cur += self._render_table(k, v, prefix=_key)
+                    cur += self._render_table(k, v, prefix=_key, delegated=delegated)
             elif isinstance(v, AoT):
                 assert k is not None
                 cur += self._render_aot(k, v, prefix=_key)