diff --git a/meta/classes-global/sstate.bbclass b/meta/classes-global/sstate.bbclass
index af93546b04..edf5c7fb65 100644
--- a/meta/classes-global/sstate.bbclass
+++ b/meta/classes-global/sstate.bbclass
@@ -529,9 +529,20 @@ def sstate_clean_manifest(manifest, d, canrace=False, prefix=None):
     entries = mfile.readlines()
     mfile.close()
 
+    recipe_sysroot = d.getVar("RECIPE_SYSROOT").rstrip("/").rsplit('/', 1)[-1]
+
     for entry in entries:
         sstate_clean_entry(entry, canrace, prefix)
 
+        # The sysroot directory stored in the manifest file might not be the
+        # same as RECIPE_SYSROOT, so the real sysroot will not be properly
+        # cleaned up on rebuild. Handle the cleanup here in order to avoid
+        # "File exists" errors during do_prepare_recipe_sysroot().
+        manifest_sysroot = entry.split("/", 1)[0] or None
+        if manifest_sysroot and manifest_sysroot != recipe_sysroot and not manifest_sysroot.endswith("-native"):
+            sysroot_entry = recipe_sysroot + "/" + entry.split("/", 1)[1]
+            sstate_clean_entry(sysroot_entry, canrace, prefix)
+
     postrm = manifest + ".postrm"
     if os.path.exists(manifest + ".postrm"):
         import subprocess