diff --git a/server/jetstream_cluster_4_test.go b/server/jetstream_cluster_4_test.go
index 77a59c7150d..cefc1182297 100644
--- a/server/jetstream_cluster_4_test.go
+++ b/server/jetstream_cluster_4_test.go
@@ -2976,20 +2976,27 @@ func TestJetStreamClusterAPILimitAdvisory(t *testing.T) {
 	// pushing to and draining the queue, so make sure we've sent enough of them
 	// to reliably trigger a drain and advisory.
 	inbox := nc.NewRespInbox()
-	for i := 0; i < runtime.GOMAXPROCS(-1)*2; i++ {
+	total := 100
+	for range total {
 		require_NoError(t, nc.PublishMsg(&nats.Msg{
 			Subject: fmt.Sprintf(JSApiConsumerListT, "TEST"),
 			Reply:   inbox,
 		}))
 	}
 
-	// Wait for the advisory to come in.
-	msg, err := sub.NextMsg(time.Second * 5)
-	require_NoError(t, err)
-	var advisory JSAPILimitReachedAdvisory
-	require_NoError(t, json.Unmarshal(msg.Data, &advisory))
-	require_Equal(t, advisory.Domain, _EMPTY_) // No JetStream domain was set.
-	require_True(t, advisory.Dropped >= 1)     // We dropped at least something.
+	for range total {
+		// Wait for the advisory to come in.
+		msg, err := sub.NextMsg(time.Second * 5)
+		require_NoError(t, err)
+		var advisory JSAPILimitReachedAdvisory
+		require_NoError(t, json.Unmarshal(msg.Data, &advisory))
+		require_Equal(t, advisory.Domain, _EMPTY_) // No JetStream domain was set.
+		if advisory.Dropped >= 1 {
+			// We are done!
+			return
+		}
+	}
+	t.Fatal("Did not get any advisory with dropped > 0")
 }
 
 func TestJetStreamClusterPendingRequestsInJsz(t *testing.T) {
diff --git a/server/opts.go b/server/opts.go
index 3cf8f23aa5e..e0c1d6a4ecc 100644
--- a/server/opts.go
+++ b/server/opts.go
@@ -5369,7 +5369,10 @@ func MergeOptions(fileOpts, flagOpts *Options) *Options {
 		mergeRoutes(&opts, flagOpts)
 	}
 	if flagOpts.JetStream {
-		fileOpts.JetStream = flagOpts.JetStream
+		opts.JetStream = flagOpts.JetStream
+	}
+	if flagOpts.StoreDir != _EMPTY_ {
+		opts.StoreDir = flagOpts.StoreDir
 	}
 	return &opts
 }
@@ -5834,6 +5837,8 @@ func ConfigureOptions(fs *flag.FlagSet, args []string, printVersion, printHelp,
 			trackExplicitVal(&FlagSnapshot.inCmdLine, "Syslog", FlagSnapshot.Syslog)
 		case "no_advertise":
 			trackExplicitVal(&FlagSnapshot.inCmdLine, "Cluster.NoAdvertise", FlagSnapshot.Cluster.NoAdvertise)
+		case "js":
+			trackExplicitVal(&FlagSnapshot.inCmdLine, "JetStream", FlagSnapshot.JetStream)
 		}
 	})
 
diff --git a/server/opts_test.go b/server/opts_test.go
index 5eca8de2e3c..8a4bf62d9dd 100644
--- a/server/opts_test.go
+++ b/server/opts_test.go
@@ -288,6 +288,8 @@ func TestMergeOverrides(t *testing.T) {
 		LameDuckDuration:      4 * time.Minute,
 		ConnectErrorReports:   86400,
 		ReconnectErrorReports: 5,
+		JetStream:             true,
+		StoreDir:              "/store/dir",
 		authBlockDefined:      true,
 		configDigest:          "sha256:314adbd9997c1183f028f5b620362daa45893da76bac746136bfb48b2fd14996",
 	}
@@ -308,6 +310,8 @@ func TestMergeOverrides(t *testing.T) {
 			NoAdvertise:    true,
 			ConnectRetries: 2,
 		},
+		JetStream: true,
+		StoreDir:  "/store/dir",
 	}
 	merged := MergeOptions(fopts, opts)
 
diff --git a/server/reload_test.go b/server/reload_test.go
index bc20f40641c..a44e6e0f0d7 100644
--- a/server/reload_test.go
+++ b/server/reload_test.go
@@ -3808,9 +3808,53 @@ func TestConfigReloadBoolFlags(t *testing.T) {
 			true,
 			func() bool { return opts.TraceVerbose },
 		},
+		// --js override
+		{
+			"jetstream_not_in_config_no_override",
+			"",
+			nil,
+			false,
+			func() bool { return opts.JetStream },
+		},
+		{
+			"jetstream_not_in_config_override_true",
+			"",
+			[]string{"--js"},
+			true,
+			func() bool { return opts.JetStream },
+		},
+		{
+			"jetstream_false_in_config_no_override",
+			"jetstream: false",
+			nil,
+			false,
+			func() bool { return opts.JetStream },
+		},
+		{
+			"jetstream_false_in_config_override_true",
+			"jetstream: false",
+			[]string{"--js"},
+			true,
+			func() bool { return opts.JetStream },
+		},
+		{
+			"jetstream_true_in_config_no_override",
+			"jetstream: true",
+			nil,
+			true,
+			func() bool { return opts.JetStream },
+		},
+		{
+			"jetstream_true_in_config_override_false",
+			"jetstream: true",
+			[]string{"--js=false"},
+			false,
+			func() bool { return opts.JetStream },
+		},
 	} {
 		t.Run(test.name, func(t *testing.T) {
-			conf := createConfFile(t, []byte(fmt.Sprintf(template, logfile, test.content)))
+			content := fmt.Sprintf(template, logfile, test.content)
+			conf := createConfFile(t, []byte(content))
 
 			fs := flag.NewFlagSet("test", flag.ContinueOnError)
 			var args []string
@@ -3829,9 +3873,15 @@ func TestConfigReloadBoolFlags(t *testing.T) {
 			if test.val() != test.expected {
 				t.Fatalf("Expected to be set to %v, got %v", test.expected, test.val())
 			}
-			if err := s.Reload(); err != nil {
-				t.Fatalf("Error on reload: %v", err)
-			}
+			// Do a config reload with a modified config file so that s.Reload()
+			// actually does something (otherwise it would not because config
+			// digest would not have changed). We could alternatively change
+			// s.opts.configDigest to the empty string.
+			reloadUpdateConfig(t, s, conf, content+`
+				max_connections: 1000
+			`)
+			// Have `opts` now point to the new options after the Reload()
+			opts = s.getOpts()
 			if test.val() != test.expected {
 				t.Fatalf("Expected to be set to %v, got %v", test.expected, test.val())
 			}