diff --git a/lib/fluent/plugin/in_dummy.rb b/lib/fluent/plugin/in_dummy.rb
index 5f1bb71c4b..648d620e55 100644
--- a/lib/fluent/plugin/in_dummy.rb
+++ b/lib/fluent/plugin/in_dummy.rb
@@ -80,7 +80,7 @@ def run
           break unless (thread_current_running? && Time.now.to_i <= current_time)
           wait(0.1) { emit(batch_num) }
         end
-        emit(residual_num)
+        emit(residual_num) if thread_current_running?
         # wait for next second
         while thread_current_running? && Time.now.to_i <= current_time
           sleep 0.01
diff --git a/lib/fluent/root_agent.rb b/lib/fluent/root_agent.rb
index 26dceb752b..45be7fac7c 100644
--- a/lib/fluent/root_agent.rb
+++ b/lib/fluent/root_agent.rb
@@ -104,7 +104,7 @@ def setup_error_label(e)
       @error_collector = error_label.event_router
     end
 
-    def lifecycle(desc: false)
+    def lifecycle(desc: false, kind_callback: nil)
       kind_or_label_list = if desc
                     [:output, :filter, @labels.values.reverse, :output_with_router, :input].flatten
                   else
@@ -127,6 +127,9 @@ def lifecycle(desc: false)
             yield instance, display_kind
           end
         end
+        if kind_callback
+          kind_callback.call
+        end
       end
     end
 
@@ -175,13 +178,18 @@ def shutdown # Fluentd's shutdown sequence is stop, before_shutdown, shutdown, a
 
       lifecycle_unsafe_sequence = ->(method, checker) {
         operation = case method
+                    when :before_shutdown then "preparing shutdown"
                     when :shutdown then "shutting down"
                     when :close    then "closing"
                     else
                       raise "BUG: unknown method name '#{method}'"
                     end
         operation_threads = []
-        lifecycle do |instance, kind|
+        callback = ->(){
+          operation_threads.each{|t| t.join }
+          operation_threads.clear
+        }
+        lifecycle(kind_callback: callback) do |instance, kind|
           t = Thread.new do
             Thread.current.abort_on_exception = true
             begin
@@ -194,12 +202,12 @@ def shutdown # Fluentd's shutdown sequence is stop, before_shutdown, shutdown, a
           end
           operation_threads << t
         end
-        operation_threads.each{|t| t.join }
       }
 
       lifecycle_safe_sequence.call(:stop, :stopped?)
 
-      lifecycle_safe_sequence.call(:before_shutdown, :before_shutdown?)
+      # before_shutdown does force_flush for output plugins: it should block, so it's unsafe operation
+      lifecycle_unsafe_sequence.call(:before_shutdown, :before_shutdown?)
 
       lifecycle_unsafe_sequence.call(:shutdown, :shutdown?)