diff --git a/src/gitingest/entrypoint.py b/src/gitingest/entrypoint.py
index f6b5c8c8..bc80c576 100644
--- a/src/gitingest/entrypoint.py
+++ b/src/gitingest/entrypoint.py
@@ -269,7 +269,7 @@ def _apply_gitignores(query: IngestionQuery) -> None:
 
     """
     for fname in (".gitignore", ".gitingestignore"):
-        query.ignore_patterns.update(load_ignore_patterns(query.local_path, filename=fname))
+        query.ignore_patterns = [*query.ignore_patterns, *load_ignore_patterns(query.local_path, filename=fname)]
 
 
 @asynccontextmanager
diff --git a/src/gitingest/utils/ignore_patterns.py b/src/gitingest/utils/ignore_patterns.py
index 5236e4d1..50af274b 100644
--- a/src/gitingest/utils/ignore_patterns.py
+++ b/src/gitingest/utils/ignore_patterns.py
@@ -168,7 +168,7 @@
 }
 
 
-def load_ignore_patterns(root: Path, filename: str) -> set[str]:
+def load_ignore_patterns(root: Path, filename: str) -> list[str]:
     """Load ignore patterns from ``filename`` found under ``root``.
 
     The loader walks the directory tree, looks for the supplied ``filename``,
@@ -185,20 +185,20 @@ def load_ignore_patterns(root: Path, filename: str) -> set[str]:
 
     Returns
     -------
-    set[str]
-        A set of ignore patterns extracted from the ``filename`` file found under the ``root`` directory.
+    list[str]
+        Ignore patterns extracted from the ``filename`` file found under the ``root`` directory.
 
     """
-    patterns: set[str] = set()
+    patterns: list[str] = []
 
     for ignore_file in root.rglob(filename):
         if ignore_file.is_file():
-            patterns.update(_parse_ignore_file(ignore_file, root))
+            patterns.extend(_parse_ignore_file(ignore_file, root))
     return patterns
 
 
-def _parse_ignore_file(ignore_file: Path, root: Path) -> set[str]:
-    """Parse an ignore file and return a set of ignore patterns.
+def _parse_ignore_file(ignore_file: Path, root: Path) -> list[str]:
+    """Parse an ignore file and return ignore patterns.
 
     Parameters
     ----------
@@ -209,11 +209,11 @@ def _parse_ignore_file(ignore_file: Path, root: Path) -> set[str]:
 
     Returns
     -------
-    set[str]
-        A set of ignore patterns.
+    list[str]
+        Ignore patterns in file order.
 
     """
-    patterns: set[str] = set()
+    patterns: list[str] = []
 
     # Path of the ignore file relative to the repository root
     rel_dir = ignore_file.parent.relative_to(root)
@@ -235,6 +235,6 @@ def _parse_ignore_file(ignore_file: Path, root: Path) -> set[str]:
                 line = line.lstrip("/")
 
             pattern_body = (base_dir / line).as_posix()
-            patterns.add(f"!{pattern_body}" if negated else pattern_body)
+            patterns.append(f"!{pattern_body}" if negated else pattern_body)
 
     return patterns
diff --git a/src/gitingest/utils/ingestion_utils.py b/src/gitingest/utils/ingestion_utils.py
index 8795b66c..a9501168 100644
--- a/src/gitingest/utils/ingestion_utils.py
+++ b/src/gitingest/utils/ingestion_utils.py
@@ -7,6 +7,7 @@
 from pathspec import PathSpec
 
 if TYPE_CHECKING:
+    from collections.abc import Iterable
     from pathlib import Path
 
 
@@ -40,7 +41,7 @@ def _should_include(path: Path, base_path: Path, include_patterns: set[str]) ->
     return spec.match_file(str(rel_path))
 
 
-def _should_exclude(path: Path, base_path: Path, ignore_patterns: set[str]) -> bool:
+def _should_exclude(path: Path, base_path: Path, ignore_patterns: Iterable[str]) -> bool:
     """Return ``True`` if ``path`` matches any of ``ignore_patterns``.
 
     Parameters
diff --git a/tests/test_gitignore_feature.py b/tests/test_gitignore_feature.py
index 68ab821a..ceb30dfd 100644
--- a/tests/test_gitignore_feature.py
+++ b/tests/test_gitignore_feature.py
@@ -48,6 +48,14 @@ def test_load_gitignore_patterns(tmp_path: Path) -> None:
         assert not pattern.startswith("#")
 
 
+def test_load_gitignore_patterns_preserves_negation_order(tmp_path: Path) -> None:
+    """Test that negated gitignore patterns keep their file order."""
+    gitignore = tmp_path / ".gitignore"
+    gitignore.write_text("*.log\n!important.log\n")
+
+    assert load_ignore_patterns(tmp_path, filename=".gitignore") == ["*.log", "!important.log"]
+
+
 @pytest.mark.asyncio
 async def test_ingest_with_gitignore(repo_path: Path) -> None:
     """Integration test for ``ingest_async()`` respecting ``.gitignore`` rules.
@@ -67,3 +75,21 @@ async def test_ingest_with_gitignore(repo_path: Path) -> None:
     # Now both files should be present.
     assert "This file should be excluded." in content_without_ignore
     assert "This file should be included." in content_without_ignore
+
+
+@pytest.mark.asyncio
+async def test_ingest_with_gitignore_negation(tmp_path: Path) -> None:
+    """Test that later negated gitignore rules can re-include files."""
+    gitignore = tmp_path / ".gitignore"
+    gitignore.write_text("*.log\n!important.log\n")
+
+    ignored_file = tmp_path / "ignored.log"
+    ignored_file.write_text("This log should be ignored.")
+
+    important_file = tmp_path / "important.log"
+    important_file.write_text("This log should be included.")
+
+    _, _, content = await ingest_async(source=str(tmp_path))
+
+    assert "This log should be ignored." not in content
+    assert "This log should be included." in content