diff --git a/.github/workflows/bsim-tests.yaml b/.github/workflows/bsim-tests.yaml
index 4739f99e68b194..2b5592b65272c6 100644
--- a/.github/workflows/bsim-tests.yaml
+++ b/.github/workflows/bsim-tests.yaml
@@ -77,6 +77,7 @@ jobs:
           git config --global user.email "bot@zephyrproject.org"
           git config --global user.name "Zephyr Bot"
           rm -fr ".git/rebase-apply"
+          rm -fr ".git/rebase-merge"
           git rebase origin/${BASE_REF}
           git clean -f -d
           git log  --pretty=oneline | head -n 10
diff --git a/.github/workflows/clang.yaml b/.github/workflows/clang.yaml
index 0d97ecc8abcade..c8da74ee317996 100644
--- a/.github/workflows/clang.yaml
+++ b/.github/workflows/clang.yaml
@@ -61,6 +61,7 @@ jobs:
           git config --global user.email "bot@zephyrproject.org"
           git config --global user.name "Zephyr Bot"
           rm -fr ".git/rebase-apply"
+          rm -fr ".git/rebase-merge"
           git rebase origin/${BASE_REF}
           git clean -f -d
           git log  --pretty=oneline | head -n 10
diff --git a/.github/workflows/coding_guidelines.yml b/.github/workflows/coding_guidelines.yml
index 97d2301a9e3c91..952056aa4da7e4 100644
--- a/.github/workflows/coding_guidelines.yml
+++ b/.github/workflows/coding_guidelines.yml
@@ -40,6 +40,8 @@ jobs:
         git config --global user.email "actions@zephyrproject.org"
         git config --global user.name "Github Actions"
         git remote -v
+        rm -fr ".git/rebase-apply"
+        rm -fr ".git/rebase-merge"
         git rebase origin/${BASE_REF}
         git clean -f -d
         source zephyr-env.sh
diff --git a/.github/workflows/compliance.yml b/.github/workflows/compliance.yml
index ecd874dd4869b9..3795101a9b2778 100644
--- a/.github/workflows/compliance.yml
+++ b/.github/workflows/compliance.yml
@@ -33,6 +33,8 @@ jobs:
         # Ensure there's no merge commits in the PR
         [[ "$(git rev-list --merges --count origin/${BASE_REF}..)" == "0" ]] || \
         (echo "::error ::Merge commits not allowed, rebase instead";false)
+        rm -fr ".git/rebase-apply"
+        rm -fr ".git/rebase-merge"
         git rebase origin/${BASE_REF}
         git clean -f -d
         # debug
diff --git a/.github/workflows/doc-build.yml b/.github/workflows/doc-build.yml
index 7564d163f81d5a..04a114195bbfcd 100644
--- a/.github/workflows/doc-build.yml
+++ b/.github/workflows/doc-build.yml
@@ -94,6 +94,8 @@ jobs:
       run: |
         git config --global user.email "actions@zephyrproject.org"
         git config --global user.name "Github Actions"
+        rm -fr ".git/rebase-apply"
+        rm -fr ".git/rebase-merge"
         git rebase origin/${BASE_REF}
         git clean -f -d
         git log --graph --oneline HEAD...${PR_HEAD}
diff --git a/.github/workflows/hello_world_multiplatform.yaml b/.github/workflows/hello_world_multiplatform.yaml
index 605cc2a903b695..f654ec71ab0930 100644
--- a/.github/workflows/hello_world_multiplatform.yaml
+++ b/.github/workflows/hello_world_multiplatform.yaml
@@ -45,6 +45,8 @@ jobs:
         run: |
           git config --global user.email "actions@zephyrproject.org"
           git config --global user.name "Github Actions"
+          rm -fr ".git/rebase-apply"
+          rm -fr ".git/rebase-merge"
           git rebase origin/${BASE_REF}
           git clean -f -d
           git log --graph --oneline HEAD...${PR_HEAD}
diff --git a/.github/workflows/scripts_tests.yml b/.github/workflows/scripts_tests.yml
index 183f3eb474be0b..2889785a3275e9 100644
--- a/.github/workflows/scripts_tests.yml
+++ b/.github/workflows/scripts_tests.yml
@@ -42,6 +42,8 @@ jobs:
         run: |
           git config --global user.email "actions@zephyrproject.org"
           git config --global user.name "Github Actions"
+          rm -fr ".git/rebase-apply"
+          rm -fr ".git/rebase-merge"
           git rebase origin/${BASE_REF}
           git clean -f -d
           git log --graph --oneline HEAD...${PR_HEAD}
diff --git a/.github/workflows/twister-prep.yaml b/.github/workflows/twister-prep.yaml
index 4c8b03a5418b69..51bc771059d695 100644
--- a/.github/workflows/twister-prep.yaml
+++ b/.github/workflows/twister-prep.yaml
@@ -67,6 +67,7 @@ jobs:
           git config --global user.email "bot@zephyrproject.org"
           git config --global user.name "Zephyr Bot"
           rm -fr ".git/rebase-apply"
+          rm -fr ".git/rebase-merge"
           git rebase origin/${BASE_REF}
           git clean -f -d
           git log  --pretty=oneline | head -n 10
diff --git a/.github/workflows/twister.yaml b/.github/workflows/twister.yaml
index 0fa810b3dd7654..f29d690dd83f61 100644
--- a/.github/workflows/twister.yaml
+++ b/.github/workflows/twister.yaml
@@ -84,6 +84,7 @@ jobs:
             git config --global user.email "bot@zephyrproject.org"
             git config --global user.name "Zephyr Builder"
             rm -fr ".git/rebase-apply"
+            rm -fr ".git/rebase-merge"
             git rebase origin/${BASE_REF}
             git clean -f -d
             git log  --pretty=oneline | head -n 10