diff --git a/run_linux.go b/run_linux.go
index 2ae374c31a..cea65caf2d 100644
--- a/run_linux.go
+++ b/run_linux.go
@@ -545,6 +545,11 @@ func (b *Builder) setupMounts(mountPoint string, spec *specs.Spec, bundlePath st
 		return nil, err
 	}
 
+	// prepare list of mount destinations which can be cleaned up safely.
+	// we can clean bindFiles, subscriptionMounts and specMounts
+	// everything other than these might have users content
+	mountArtifacts.RunMountTargets = append(append(append(mountArtifacts.RunMountTargets, cleanableDestinationListFromMounts(bindFileMounts)...), cleanableDestinationListFromMounts(subscriptionMounts)...), cleanableDestinationListFromMounts(specMounts)...)
+
 	allMounts := util.SortMounts(append(append(append(append(append(append(volumes, builtins...), runMounts...), subscriptionMounts...), bindFileMounts...), specMounts...), sysfsMount...))
 	// Add them all, in the preferred order, except where they conflict with something that was previously added.
 	for _, mount := range allMounts {
@@ -561,6 +566,23 @@ func (b *Builder) setupMounts(mountPoint string, spec *specs.Spec, bundlePath st
 	return mountArtifacts, nil
 }
 
+// Destinations which can be cleaned up after every RUN
+func cleanableDestinationListFromMounts(mounts []spec.Mount) []string {
+	mountDest := []string{}
+	for _, mount := range mounts {
+		// Add all destination to mountArtifacts so that they can be cleaned up later
+		if mount.Destination != "" {
+			// we dont want to remove destinations with  /etc, /dev, /sys, /proc as rootfs already contains these files
+			// and unionfs will create a `whiteout` i.e `.wh` files on removal of overlapping files from these directories.
+			// everything other than these will be cleanedup
+			if !strings.HasPrefix(mount.Destination, "/etc") && !strings.HasPrefix(mount.Destination, "/dev") && !strings.HasPrefix(mount.Destination, "/sys") && !strings.HasPrefix(mount.Destination, "/proc") {
+				mountDest = append(mountDest, mount.Destination)
+			}
+		}
+	}
+	return mountDest
+}
+
 // addResolvConf copies files from host and sets them up to bind mount into container
 func (b *Builder) addResolvConf(rdir string, chownOpts *idtools.IDPair, dnsServers, dnsSearch, dnsOptions []string, namespaceOptions define.NamespaceOptions) (string, error) {
 	resolvConf := "/etc/resolv.conf"
diff --git a/tests/bud.bats b/tests/bud.bats
index 98c7eebb60..30b1704a28 100644
--- a/tests/bud.bats
+++ b/tests/bud.bats
@@ -3446,3 +3446,55 @@ _EOF
 
   run_buildah rmi -f ${target}
 }
+
+@test "bud with run should not leave mounts behind cleanup test" {
+  skip_if_in_container
+  run which podman
+  if [[ $status -ne 0 ]]; then
+    skip "podman is not installed"
+  fi
+
+  # Create target dir where we will export tar
+  target=cleanable
+  mkdir ${TESTDIR}/${target}
+
+  # Build and export container to tar
+  run_buildah build --no-cache --signature-policy ${TESTSDIR}/policy.json -t ${target} -f ${TESTSDIR}/bud/containerfile/Containerfile.in ${TESTSDIR}/bud/containerfile
+  podman export $(podman create --name ${target} ${target}) --output=${TESTDIR}/${target}.tar
+
+  # We are done exporting so remove images and containers which are not needed
+  podman rm -f ${target}
+  run_buildah rmi ${target}
+
+  # Explode tar
+  tar -xf ${TESTDIR}/${target}.tar -C ${TESTDIR}/${target}
+  count=$(ls -A ${TESTDIR}/${target}/run | wc -l)
+  ## exported /run should be empty
+  assert "$count" == "0"
+}
+
+@test "bud with custom files in /run/ should persist cleanup test" {
+  skip_if_in_container
+  run which podman
+  if [[ $status -ne 0 ]]; then
+    skip "podman is not installed"
+  fi
+
+  # Create target dir where we will export tar
+  target=cleanable
+  mkdir ${TESTDIR}/${target}
+
+  # Build and export container to tar
+  run_buildah build --no-cache --signature-policy ${TESTSDIR}/policy.json -t ${target} -f ${TESTSDIR}/bud/add-run-dir
+  podman export $(podman create --name ${target} ${target}) --output=${TESTDIR}/${target}.tar
+
+  # We are done exporting so remove images and containers which are not needed
+  podman rm -f ${target}
+  run_buildah rmi ${target}
+
+  # Explode tar
+  tar -xf ${TESTDIR}/${target}.tar -C ${TESTDIR}/${target}
+  count=$(ls -A ${TESTDIR}/${target}/run | wc -l)
+  ## exported /run should not be empty
+  assert "$count" == "1"
+}
diff --git a/tests/bud/add-run-dir/Dockerfile b/tests/bud/add-run-dir/Dockerfile
new file mode 100644
index 0000000000..d4b4ebe348
--- /dev/null
+++ b/tests/bud/add-run-dir/Dockerfile
@@ -0,0 +1,2 @@
+FROM alpine
+RUN touch /run/hello