diff --git a/pkg/agent/run.go b/pkg/agent/run.go
index 753d01dba31c..1229c2194afa 100644
--- a/pkg/agent/run.go
+++ b/pkg/agent/run.go
@@ -28,6 +28,7 @@ import (
 	"github.com/k3s-io/k3s/pkg/nodeconfig"
 	"github.com/k3s-io/k3s/pkg/rootless"
 	"github.com/k3s-io/k3s/pkg/util"
+	"github.com/k3s-io/k3s/pkg/version"
 	"github.com/pkg/errors"
 	"github.com/sirupsen/logrus"
 	v1 "k8s.io/api/core/v1"
@@ -146,8 +147,13 @@ func run(ctx context.Context, cfg cmds.Agent, proxy proxy.Proxy) error {
 		}
 	}
 
-	os.Setenv("NOTIFY_SOCKET", notifySocket)
-	systemd.SdNotify(true, "READY=1\n")
+	// By default, the server is responsible for notifying systemd
+	// On agent-only nodes, the agent will notify systemd
+	if notifySocket != "" {
+		logrus.Info(version.Program + " agent is up and running")
+		os.Setenv("NOTIFY_SOCKET", notifySocket)
+		systemd.SdNotify(true, "READY=1\n")
+	}
 
 	<-ctx.Done()
 	return ctx.Err()
diff --git a/pkg/cli/server/server.go b/pkg/cli/server/server.go
index fde31569c488..8d50d8c1feff 100644
--- a/pkg/cli/server/server.go
+++ b/pkg/cli/server/server.go
@@ -444,6 +444,7 @@ func run(app *cli.Context, cfg *cmds.Server, leaderControllers server.CustomCont
 	logrus.Info("Starting " + version.Program + " " + app.App.Version)
 
 	notifySocket := os.Getenv("NOTIFY_SOCKET")
+	os.Unsetenv("NOTIFY_SOCKET")
 
 	ctx := signals.SetupSignalContext()
 
@@ -455,16 +456,16 @@ func run(app *cli.Context, cfg *cmds.Server, leaderControllers server.CustomCont
 		if !serverConfig.ControlConfig.DisableAPIServer {
 			<-serverConfig.ControlConfig.Runtime.APIServerReady
 			logrus.Info("Kube API server is now running")
-		} else {
+			serverConfig.ControlConfig.Runtime.StartupHooksWg.Wait()
+		}
+		if !serverConfig.ControlConfig.DisableETCD {
 			<-serverConfig.ControlConfig.Runtime.ETCDReady
 			logrus.Info("ETCD server is now running")
 		}
 
 		logrus.Info(version.Program + " is up and running")
-		if (cfg.DisableAgent || cfg.DisableAPIServer) && notifySocket != "" {
-			os.Setenv("NOTIFY_SOCKET", notifySocket)
-			systemd.SdNotify(true, "READY=1\n")
-		}
+		os.Setenv("NOTIFY_SOCKET", notifySocket)
+		systemd.SdNotify(true, "READY=1\n")
 	}()
 
 	url := fmt.Sprintf("https://%s:%d", serverConfig.ControlConfig.BindAddressOrLoopback(false), serverConfig.ControlConfig.SupervisorPort)
diff --git a/pkg/daemons/config/types.go b/pkg/daemons/config/types.go
index d296761be9fe..b7cf18b9e22a 100644
--- a/pkg/daemons/config/types.go
+++ b/pkg/daemons/config/types.go
@@ -8,6 +8,7 @@ import (
 	"net/http"
 	"sort"
 	"strings"
+	"sync"
 	"time"
 
 	"github.com/k3s-io/k3s/pkg/util"
@@ -269,6 +270,7 @@ type ControlRuntime struct {
 	APIServerReady                      <-chan struct{}
 	AgentReady                          <-chan struct{}
 	ETCDReady                           <-chan struct{}
+	StartupHooksWg                      *sync.WaitGroup
 	ClusterControllerStart              func(ctx context.Context) error
 	LeaderElectedClusterControllerStart func(ctx context.Context) error
 
diff --git a/pkg/server/secrets-encrypt.go b/pkg/server/secrets-encrypt.go
index 610c73b1cd63..0db520bef8fd 100644
--- a/pkg/server/secrets-encrypt.go
+++ b/pkg/server/secrets-encrypt.go
@@ -186,6 +186,10 @@ func encryptionConfigHandler(ctx context.Context, server *config.Control) http.H
 			genErrorMessage(resp, http.StatusBadRequest, err)
 			return
 		}
+		// If a user kills the k3s server immediately after this call, we run into issues where the files
+		// have not yet been written. This sleep ensures that things have time to sync to disk before
+		// the request completes.
+		time.Sleep(1 * time.Second)
 		resp.WriteHeader(http.StatusOK)
 	})
 }
diff --git a/pkg/server/server.go b/pkg/server/server.go
index ffdcb13a15ac..97f639ba201b 100644
--- a/pkg/server/server.go
+++ b/pkg/server/server.go
@@ -64,6 +64,8 @@ func StartServer(ctx context.Context, config *Config, cfg *cmds.Server) error {
 	wg.Add(len(config.StartupHooks))
 
 	config.ControlConfig.Runtime.Handler = router(ctx, config, cfg)
+	config.ControlConfig.Runtime.StartupHooksWg = wg
+
 	shArgs := cmds.StartupHookArgs{
 		APIServerReady:  config.ControlConfig.Runtime.APIServerReady,
 		KubeConfigAdmin: config.ControlConfig.Runtime.KubeConfigAdmin,
@@ -79,7 +81,7 @@ func StartServer(ctx context.Context, config *Config, cfg *cmds.Server) error {
 	if config.ControlConfig.DisableAPIServer {
 		go setETCDLabelsAndAnnotations(ctx, config)
 	} else {
-		go startOnAPIServerReady(ctx, wg, config)
+		go startOnAPIServerReady(ctx, config)
 	}
 
 	if err := printTokens(&config.ControlConfig); err != nil {
@@ -89,18 +91,18 @@ func StartServer(ctx context.Context, config *Config, cfg *cmds.Server) error {
 	return writeKubeConfig(config.ControlConfig.Runtime.ServerCA, config)
 }
 
-func startOnAPIServerReady(ctx context.Context, wg *sync.WaitGroup, config *Config) {
+func startOnAPIServerReady(ctx context.Context, config *Config) {
 	select {
 	case <-ctx.Done():
 		return
 	case <-config.ControlConfig.Runtime.APIServerReady:
-		if err := runControllers(ctx, wg, config); err != nil {
+		if err := runControllers(ctx, config); err != nil {
 			logrus.Fatalf("failed to start controllers: %v", err)
 		}
 	}
 }
 
-func runControllers(ctx context.Context, wg *sync.WaitGroup, config *Config) error {
+func runControllers(ctx context.Context, config *Config) error {
 	controlConfig := &config.ControlConfig
 
 	sc, err := NewContext(ctx, controlConfig.Runtime.KubeConfigAdmin)
@@ -108,7 +110,7 @@ func runControllers(ctx context.Context, wg *sync.WaitGroup, config *Config) err
 		return errors.Wrap(err, "failed to create new server context")
 	}
 
-	wg.Wait()
+	controlConfig.Runtime.StartupHooksWg.Wait()
 	if err := stageFiles(ctx, sc, controlConfig); err != nil {
 		return errors.Wrap(err, "failed to stage files")
 	}