diff --git a/bin/pt-agent b/bin/pt-agent
index 8a1c4d60..ece2fc54 100755
--- a/bin/pt-agent
+++ b/bin/pt-agent
@@ -4975,13 +4975,20 @@ sub _log {
    return;
 }
 
-sub DESTROY {
+sub stop_online_logging {
    my $self = shift;
-   if ( $self->online_logging ) {
+   if ( $self->_thread && $self->_thread->is_running() ) {
       my @stop :shared = (undef, undef);
       $self->_message_queue->enqueue(\@stop);  # stop the thread
       $self->_thread->join();
    }
+   $self->online_logging(0);
+   return;
+}
+
+sub DESTROY {
+   my $self = shift;
+   $self->stop_online_logging();
    return;
 }
 
@@ -5365,8 +5372,8 @@ sub main {
 
    $logger->info("pt-agent exit $exit_status, oktorun $oktorun");
 
-   # Cause Logger::DESTORY to be called.
-   $logger = undef;
+   $logger->stop_online_logging();
+   $logger->info('Waiting for logging thread to stop...');
 
    return $exit_status;
 }
diff --git a/lib/Percona/Agent/Logger.pm b/lib/Percona/Agent/Logger.pm
index 2b59ebc7..b291abef 100644
--- a/lib/Percona/Agent/Logger.pm
+++ b/lib/Percona/Agent/Logger.pm
@@ -207,13 +207,20 @@ sub _log {
    return;
 }
 
-sub DESTROY {
+sub stop_online_logging {
    my $self = shift;
-   if ( $self->online_logging ) {
+   if ( $self->_thread && $self->_thread->is_running() ) {
       my @stop :shared = (undef, undef);
       $self->_message_queue->enqueue(\@stop);  # stop the thread
       $self->_thread->join();
    }
+   $self->online_logging(0);
+   return;
+}
+
+sub DESTROY {
+   my $self = shift;
+   $self->stop_online_logging();
    return;
 }