diff --git a/docs/project/changelog.md b/docs/project/changelog.md
index 33fcc8b12..9950c5ae6 100644
--- a/docs/project/changelog.md
+++ b/docs/project/changelog.md
@@ -84,7 +84,7 @@ myst:
 - Upgraded `bokeh` to 3.6.0 {pr}`4888`, {pr}`5047`, {pr}`5118`
 - Upgraded `pandas` to 2.2.2 {pr}`4893`
 - Upgraded `zengl` to 2.5.0 {pr}`4894`
-- Upgraded `protobuf` to 5.27.3 {pr}`4601`
+- Upgraded `protobuf` to 5.29.0 {pr}`5233`
 - Upgraded `sourmash` to 4.8.11 {pr}`4980`
 - Upgraded `scipy` to 1.14.1 {pr}`4719`, {pr}`5011`, {pr}`5012`, {pr}`5031`
 - Upgraded `scikit-image` to 0.24.0 {pr}`5003`
diff --git a/packages/protobuf/meta.yaml b/packages/protobuf/meta.yaml
index 02a478e12..f8a480ad4 100644
--- a/packages/protobuf/meta.yaml
+++ b/packages/protobuf/meta.yaml
@@ -1,14 +1,14 @@
 package:
   name: protobuf
-  version: 5.28.3
+  version: 5.29.0
   top-level:
     - google
 
 source:
-  url: https://files.pythonhosted.org/packages/74/6e/e69eb906fddcb38f8530a12f4b410699972ab7ced4e21524ece9d546ac27/protobuf-5.28.3.tar.gz
-  sha256: 64badbc49180a5e401f373f9ce7ab1d18b63f7dd4a9cdc43c92b9f0b481cef7b
+  url: https://files.pythonhosted.org/packages/6a/bb/8e59a30b83102a37d24f907f417febb58e5f544d4f124dd1edcd12e078bf/protobuf-5.29.0.tar.gz
+  sha256: 445a0c02483869ed8513a585d80020d012c6dc60075f96fa0563a724987b1001
   patches:
-    - patches/0001-Fix-signature-of-PyUpb_MessageMeta_Clear.patch
+    - patches/0001-Fix-indentation-in-service-py.patch
 
 about:
   home: https://github.com/protocolbuffers/protobuf
diff --git a/packages/protobuf/patches/0001-Fix-indentation-in-service-py.patch b/packages/protobuf/patches/0001-Fix-indentation-in-service-py.patch
new file mode 100644
index 000000000..2c4b1e034
--- /dev/null
+++ b/packages/protobuf/patches/0001-Fix-indentation-in-service-py.patch
@@ -0,0 +1,13 @@
+diff --git a/google/protobuf/service.py b/google/protobuf/service.py
+index 8002c04..795b602 100644
+--- a/google/protobuf/service.py
++++ b/google/protobuf/service.py
+@@ -75,7 +75,7 @@ class Service(object):
+      Further details about the failure can be found by querying the
+      RpcController.
+     """
+-   raise NotImplementedError
++    raise NotImplementedError
+ 
+   def GetRequestClass(self, method_descriptor):
+     """Returns the class of the request message for the specified method.
diff --git a/packages/protobuf/patches/0001-Fix-signature-of-PyUpb_MessageMeta_Clear.patch b/packages/protobuf/patches/0001-Fix-signature-of-PyUpb_MessageMeta_Clear.patch
deleted file mode 100644
index 8b7563866..000000000
--- a/packages/protobuf/patches/0001-Fix-signature-of-PyUpb_MessageMeta_Clear.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From b618f806a9c9a7fec79caedb218c32991c2fbf98 Mon Sep 17 00:00:00 2001
-From: Hood Chatham <roberthoodchatham@gmail.com>
-Date: Tue, 27 Aug 2024 12:08:26 +0200
-Subject: [PATCH] Fix signature of `PyUpb_MessageMeta_Clear`
-
-A `tp_clear` function should have signature `int f(PyObject*)`. The presence of
-erroneous extra parameters leads to undefined behavior as indicated in the C
-specification 6.3.2.3.8. In WebAssembly builds, this causes crashes.
-https://www.open-std.org/jtc1/sc22/wg14/www/docs/n1256.pdf#page=60
-
-Upstream PR:
-https://github.com/protocolbuffers/protobuf/pull/17959
----
- python/message.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/python/message.c b/python/message.c
-index c81b43b8d..5ad1b06eb 100644
---- a/python/message.c
-+++ b/python/message.c
-@@ -2025,7 +2025,7 @@ static int PyUpb_MessageMeta_Traverse(PyObject* self, visitproc visit,
-   return cpython_bits.type_traverse(self, visit, arg);
- }
- 
--static int PyUpb_MessageMeta_Clear(PyObject* self, visitproc visit, void* arg) {
-+static int PyUpb_MessageMeta_Clear(PyObject* self) {
-   PyUpb_MessageMeta* meta = PyUpb_GetMessageMeta(self);
-   Py_CLEAR(meta->py_message_descriptor);
-   return cpython_bits.type_clear(self);
--- 
-2.34.1
-