diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8a62ab7840..1c075af80b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -57,6 +57,8 @@ Unreleased changes template.
 {#v0-0-0-fixed}
 ### Fixed
 * (pypi) The `ppc64le` is now pointing to the right target in the `platforms` package.
+* (gazelle) No longer incorrectly merge `py_binary` targets during partial updates in 
+  `file` generation mode. Fixed in [#2619](https://github.com/bazelbuild/rules_python/pull/2619).
 
 {#v0-0-0-added}
 ### Added
diff --git a/gazelle/python/kinds.go b/gazelle/python/kinds.go
index a9483372e2..7a0639abd3 100644
--- a/gazelle/python/kinds.go
+++ b/gazelle/python/kinds.go
@@ -32,7 +32,8 @@ func (*Python) Kinds() map[string]rule.KindInfo {
 
 var pyKinds = map[string]rule.KindInfo{
 	pyBinaryKind: {
-		MatchAny: true,
+		MatchAny: false,
+		MatchAttrs: []string{"srcs"},
 		NonEmptyAttrs: map[string]bool{
 			"deps":    true,
 			"main":    true,
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/BUILD.in b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/BUILD.in
new file mode 100644
index 0000000000..63b547f0b3
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/BUILD.in
@@ -0,0 +1,9 @@
+load("@rules_python//python:defs.bzl", "py_binary")
+
+# gazelle:python_generation_mode file
+
+py_binary(
+    name = "a",
+    srcs = ["a.py"],
+    visibility = ["//:__subpackages__"],
+)
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/BUILD.out b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/BUILD.out
new file mode 100644
index 0000000000..8f49cccd9f
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/BUILD.out
@@ -0,0 +1,15 @@
+load("@rules_python//python:defs.bzl", "py_binary")
+
+# gazelle:python_generation_mode file
+
+py_binary(
+    name = "a",
+    srcs = ["a.py"],
+    visibility = ["//:__subpackages__"],
+)
+
+py_binary(
+    name = "b",
+    srcs = ["b.py"],
+    visibility = ["//:__subpackages__"],
+)
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/README.md b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/README.md
new file mode 100644
index 0000000000..5aa499f4ad
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/README.md
@@ -0,0 +1,3 @@
+# Partial update with multiple per-file binaries
+
+This test case asserts that when there are multiple binaries in a package, and no __main__.py, and the BUILD file already includes a py_binary for one of the files, a py_binary is generated for the other file.
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/WORKSPACE b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/WORKSPACE
new file mode 100644
index 0000000000..faff6af87a
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/WORKSPACE
@@ -0,0 +1 @@
+# This is a Bazel workspace for the Gazelle test data.
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/a.py b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/a.py
new file mode 100644
index 0000000000..9c97da4809
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/a.py
@@ -0,0 +1,2 @@
+if __name__ == "__main__":
+    print("Hello, world!")
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/b.py b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/b.py
new file mode 100644
index 0000000000..9c97da4809
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/b.py
@@ -0,0 +1,2 @@
+if __name__ == "__main__":
+    print("Hello, world!")
diff --git a/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/test.yaml b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/test.yaml
new file mode 100644
index 0000000000..346ecd7ae8
--- /dev/null
+++ b/gazelle/python/testdata/binary_without_entrypoint_per_file_generation_partial_update/test.yaml
@@ -0,0 +1,17 @@
+# Copyright 2025 The Bazel Authors. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+---
+expect:
+  exit_code: 0