diff -r 01c5097cf1cd src/hotspot/share/gc/shenandoah/shenandoahControlThread.cpp
--- a/src/hotspot/share/gc/shenandoah/shenandoahControlThread.cpp	Mon Aug 17 11:36:09 2020 +0200
+++ b/src/hotspot/share/gc/shenandoah/shenandoahControlThread.cpp	Mon Aug 17 19:14:37 2020 -0400
@@ -424,6 +424,11 @@
 
     // Update references freed up collection set, kick the cleanup to reclaim the space.
     heap->entry_cleanup_complete();
+  } else {
+    // concurrent weak/strong root flags are unset concurrently, we depend on init-updateref pause above
+    // to make them visible to mutators before gc cycle is completed.
+    // In this case, init-updateref pause is not executed, we need to perform a handshake to complete the cycle.
+    heap->entry_finish_roots();
   }
 
   // Cycle is complete
diff -r 01c5097cf1cd src/hotspot/share/gc/shenandoah/shenandoahHeap.cpp
--- a/src/hotspot/share/gc/shenandoah/shenandoahHeap.cpp	Mon Aug 17 11:36:09 2020 +0200
+++ b/src/hotspot/share/gc/shenandoah/shenandoahHeap.cpp	Mon Aug 17 19:14:37 2020 -0400
@@ -1821,8 +1821,7 @@
     // Perform handshake to flush out dead oops
     {
       ShenandoahTimingsTracker t(ShenandoahPhaseTimings::conc_weak_roots_rendezvous);
-      ShenandoahRendezvousClosure cl;
-      Handshake::execute(&cl);
+      rendezvous_threads();
     }
   }
 }
@@ -1842,6 +1841,15 @@
   set_concurrent_strong_root_in_progress(false);
 }
 
+void ShenandoahHeap::op_finish_roots() {
+  rendezvous_threads();
+}
+
+void ShenandoahHeap::rendezvous_threads() {
+  ShenandoahRendezvousClosure cl;
+  Handshake::execute(&cl);
+}
+
 class ShenandoahResetUpdateRegionStateClosure : public ShenandoahHeapRegionClosure {
 private:
   ShenandoahMarkingContext* const _ctx;
@@ -2900,6 +2908,17 @@
   op_cleanup_early();
 }
 
+void ShenandoahHeap::entry_finish_roots() {
+  static const char* msg = "Finish Concurrent roots";
+  ShenandoahConcurrentPhase gc_phase(msg, ShenandoahPhaseTimings::conc_finish_roots);
+  EventMark em("%s", msg);
+
+  // This phase does not use workers, no need for setup
+
+  try_inject_alloc_failure();
+  op_finish_roots();
+}
+
 void ShenandoahHeap::entry_cleanup_complete() {
   static const char* msg = "Concurrent cleanup";
   ShenandoahConcurrentPhase gc_phase(msg, ShenandoahPhaseTimings::conc_cleanup_complete, true /* log_heap_usage */);
diff -r 01c5097cf1cd src/hotspot/share/gc/shenandoah/shenandoahHeap.hpp
--- a/src/hotspot/share/gc/shenandoah/shenandoahHeap.hpp	Mon Aug 17 11:36:09 2020 +0200
+++ b/src/hotspot/share/gc/shenandoah/shenandoahHeap.hpp	Mon Aug 17 19:14:37 2020 -0400
@@ -386,6 +386,7 @@
   void entry_class_unloading();
   void entry_strong_roots();
   void entry_cleanup_early();
+  void entry_finish_roots();
   void entry_evac();
   void entry_updaterefs();
   void entry_cleanup_complete();
@@ -409,12 +410,15 @@
   void op_class_unloading();
   void op_strong_roots();
   void op_cleanup_early();
+  void op_finish_roots();
   void op_conc_evac();
   void op_stw_evac();
   void op_updaterefs();
   void op_cleanup_complete();
   void op_uncommit(double shrink_before);
 
+  void rendezvous_threads();
+
   // Messages for GC trace events, they have to be immortal for
   // passing around the logging/tracing systems
   const char* init_mark_event_message() const;
diff -r 01c5097cf1cd src/hotspot/share/gc/shenandoah/shenandoahPhaseTimings.hpp
--- a/src/hotspot/share/gc/shenandoah/shenandoahPhaseTimings.hpp	Mon Aug 17 11:36:09 2020 +0200
+++ b/src/hotspot/share/gc/shenandoah/shenandoahPhaseTimings.hpp	Mon Aug 17 19:14:37 2020 -0400
@@ -99,6 +99,7 @@
   f(conc_class_unload_purge_cldg,                   "    CLDG")                        \
   f(conc_class_unload_purge_ec,                     "    Exception Caches")            \
   f(conc_strong_roots,                              "Concurrent Strong Roots")         \
+  f(conc_finish_roots,                              "Finish Concurrent Roots")         \
   SHENANDOAH_PAR_PHASE_DO(conc_strong_roots_,       "  CSR: ", f)                      \
   f(conc_evac,                                      "Concurrent Evacuation")           \
                                                                                        \