diff --git a/pkg/pkg.mk b/pkg/pkg.mk
index 626610a924..b159535eea 100644
--- a/pkg/pkg.mk
+++ b/pkg/pkg.mk
@@ -38,21 +38,25 @@ ifeq ($(QUIET),1)
   GIT_QUIET ?= --quiet
 endif
 
+# Use explicit '--git-dir' and '--work-tree' to prevent issues when the
+# directory is not a git repository for any reason (clean -xdff or others)
+GIT_IN_PKG = git -C $(PKG_BUILDDIR) --git-dir=.git --work-tree=.
+
 GITFLAGS ?= -c user.email=buildsystem@riot -c user.name="RIOT buildsystem"
 GITAMFLAGS ?= $(GIT_QUIET) --no-gpg-sign --ignore-whitespace --whitespace=nowarn
 
 ifneq (,$(wildcard $(PKG_DIR)/patches))
 $(PKG_BUILDDIR)/.git-patched: git-ensure-version $(PKG_DIR)/Makefile $(PKG_DIR)/patches/*.patch
-	$(Q)git -C $(PKG_BUILDDIR) checkout $(GIT_QUIET) -f $(PKG_VERSION)
-	$(Q)git $(GITFLAGS) -C $(PKG_BUILDDIR) am $(GITAMFLAGS) "$(PKG_DIR)"/patches/*.patch
+	$(Q)$(GIT_IN_PKG) checkout $(GIT_QUIET) -f $(PKG_VERSION)
+	$(Q)$(GIT_IN_PKG) $(GITFLAGS) am $(GITAMFLAGS) "$(PKG_DIR)"/patches/*.patch
 	$(Q)touch $@
 endif
 
 git-ensure-version: $(PKG_BUILDDIR)/.git-downloaded
-	@if [ $(shell git -C $(PKG_BUILDDIR) rev-parse HEAD) != $(PKG_VERSION) ] ; then \
-		git -C $(PKG_BUILDDIR) clean $(GIT_QUIET) -xdff ; \
-		git -C $(PKG_BUILDDIR) fetch $(GIT_QUIET) "$(PKG_URL)" "$(PKG_VERSION)" ; \
-		git -C $(PKG_BUILDDIR) checkout $(GIT_QUIET) -f $(PKG_VERSION) ; \
+	@if [ $(shell $(GIT_IN_PKG) rev-parse HEAD) != $(PKG_VERSION) ] ; then \
+		$(GIT_IN_PKG) clean $(GIT_QUIET) -xdff ; \
+		$(GIT_IN_PKG) fetch $(GIT_QUIET) "$(PKG_URL)" "$(PKG_VERSION)" ; \
+		$(GIT_IN_PKG) checkout $(GIT_QUIET) -f $(PKG_VERSION) ; \
 		touch $(PKG_BUILDDIR)/.git-downloaded ; \
 	fi
 
@@ -65,8 +69,8 @@ $(PKG_BUILDDIR)/.git-downloaded:
 clean::
 	@test -d $(PKG_BUILDDIR) && { \
 		rm $(PKG_BUILDDIR)/.git-patched ; \
-		git -C $(PKG_BUILDDIR) clean -f ; \
-		git -C $(PKG_BUILDDIR) checkout "$(PKG_VERSION)"; \
+		$(GIT_IN_PKG) clean -f ; \
+		$(GIT_IN_PKG) checkout "$(PKG_VERSION)"; \
 		make $(PKG_BUILDDIR)/.git-patched ; \
 		touch $(PKG_BUILDDIR)/.git-downloaded ; \
 	} > /dev/null 2>&1 || true