diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c825d40596..d49ef98280 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,12 +12,16 @@ repos:
         # 2 - any file matching *test*/*expected* (for host tests, if possible use this naming pattern always)
         # 3 - any directory named 'testdata'
         # 4 - IDF monitor test data
+        # 5 - protobuf auto-generated files
         exclude: &whitespace_excludes |
           (?x)^(
             .+\.(md|rst|map|bin)|
             .+test.*\/.*expected.*|
             .+\/testdata\/.+|
-            .+test_idf_monitor\/tests\/.+
+            .+test_idf_monitor\/tests\/.+|
+            .*_pb2.py|
+            .*.pb-c.h|
+            .*.pb-c.c
           )$
       - id: end-of-file-fixer
         exclude: *whitespace_excludes
@@ -35,6 +39,11 @@ repos:
     hooks:
       - id: isort
         name: isort (python)
+        exclude: >
+          (?x)^(
+              .*_pb2.py
+          )$
+
   - repo: local
     hooks:
       - id: check-executables
@@ -95,6 +104,10 @@ repos:
         additional_dependencies:
           - 'mypy==0.800'
           - 'mypy-extensions==0.4.3'
+        exclude: >
+          (?x)^(
+              .*_pb2.py
+          )$
         language: python
         types: [python]
       - id: check-tools-files-patterns
diff --git a/tools/ci/sonar_exclude_list.txt b/tools/ci/sonar_exclude_list.txt
index a91e445f52..bd53c27d8f 100644
--- a/tools/ci/sonar_exclude_list.txt
+++ b/tools/ci/sonar_exclude_list.txt
@@ -13,3 +13,11 @@ components/freertos/include/freertos/*.h
 # wpa_supplicant upstream code
 components/wpa_supplicant/src/**
 components/wpa_supplicant/include/**
+
+# Protobuf auto-generated files
+components/esp_local_ctrl/proto-c/**
+components/esp_local_ctrl/python/**
+components/protocomm/proto-c/**
+components/protocomm/python/**
+components/wifi_provisioning/proto-c/**
+components/wifi_provisioning/python/**