diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index edcacb2c9c5a..c8d3140dbfca 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -60,6 +60,7 @@ https://github.com/elastic/beats/compare/v8.2.0\...main[Check the HEAD diff]
 - Fix concurrent map writes when system/process code called from reporter code {pull}32491[32491]
 - Fix panics when a processor is closed twice {pull}34647[34647]
 - Update elastic-agent-system-metrics to v0.4.6 to allow builds on mips platforms. {pull}34674[34674]
+- Fix Beats started by agent do not respect the allow_older_versions: true configuration flag {issue}34227[34227] {pull}34964[34964]
 
 *Auditbeat*
 
diff --git a/libbeat/cmd/instance/beat.go b/libbeat/cmd/instance/beat.go
index 7d537c97db3a..57064b2e7089 100644
--- a/libbeat/cmd/instance/beat.go
+++ b/libbeat/cmd/instance/beat.go
@@ -329,7 +329,10 @@ func (b *Beat) createBeater(bt beat.Creator) (beat.Beater, error) {
 	logSystemInfo(b.Info)
 	logp.Info("Setup Beat: %s; Version: %s", b.Info.Beat, b.Info.Version)
 
-	b.checkElasticsearchVersion()
+	err = b.registerESVersionCheckCallback()
+	if err != nil {
+		return nil, err
+	}
 
 	err = b.registerESIndexManagement()
 	if err != nil {
@@ -981,15 +984,18 @@ func (b *Beat) loadDashboards(ctx context.Context, force bool) error {
 	return nil
 }
 
-// checkElasticsearchVersion registers a global callback to make sure ES instance we are connecting
+// registerESVersionCheckCallback registers a global callback to make sure ES instance we are connecting
 // to is at least on the same version as the Beat.
 // If the check is disabled or the output is not Elasticsearch, nothing happens.
-func (b *Beat) checkElasticsearchVersion() {
-	if b.isConnectionToOlderVersionAllowed() {
-		return
-	}
+func (b *Beat) registerESVersionCheckCallback() error {
+	_, err := elasticsearch.RegisterGlobalCallback(func(conn *eslegclient.Connection) error {
+		if !isElasticsearchOutput(b.Config.Output.Name()) {
+			return errors.New("Elasticsearch output is not configured")
+		}
+		if b.isConnectionToOlderVersionAllowed() {
+			return nil
+		}
 
-	_, _ = elasticsearch.RegisterGlobalCallback(func(conn *eslegclient.Connection) error {
 		esVersion := conn.GetVersion()
 		beatVersion, err := libversion.New(b.Info.Version)
 		if err != nil {
@@ -1000,6 +1006,8 @@ func (b *Beat) checkElasticsearchVersion() {
 		}
 		return nil
 	})
+
+	return err
 }
 
 func (b *Beat) isConnectionToOlderVersionAllowed() bool {
@@ -1035,13 +1043,28 @@ func (b *Beat) indexSetupCallback() elasticsearch.ConnectCallback {
 }
 
 func (b *Beat) makeOutputReloader(outReloader pipeline.OutputReloader) reload.Reloadable {
-	return reload.ReloadableFunc(func(config *reload.ConfigWithMeta) error {
+	return reload.ReloadableFunc(func(update *reload.ConfigWithMeta) error {
+		if update == nil {
+			return nil
+		}
+
 		if b.OutputConfigReloader != nil {
-			if err := b.OutputConfigReloader.Reload(config); err != nil {
+			if err := b.OutputConfigReloader.Reload(update); err != nil {
 				return err
 			}
 		}
-		return outReloader.Reload(config, b.createOutput)
+
+		// we need to update the output configuration because
+		// some callbacks are relying on it to be up to date.
+		// e.g. the Elasticsearch version validation
+		if update.Config != nil {
+			err := b.Config.Output.Unpack(update.Config)
+			if err != nil {
+				return err
+			}
+		}
+
+		return outReloader.Reload(update, b.createOutput)
 	})
 }
 
diff --git a/libbeat/cmd/instance/beat_test.go b/libbeat/cmd/instance/beat_test.go
index 3737b5099647..6520767d5502 100644
--- a/libbeat/cmd/instance/beat_test.go
+++ b/libbeat/cmd/instance/beat_test.go
@@ -26,6 +26,9 @@ import (
 	"testing"
 
 	"github.com/elastic/beats/v7/libbeat/cfgfile"
+	"github.com/elastic/beats/v7/libbeat/common/reload"
+	"github.com/elastic/beats/v7/libbeat/outputs"
+	"github.com/elastic/elastic-agent-libs/config"
 
 	"github.com/gofrs/uuid"
 	"github.com/stretchr/testify/assert"
@@ -224,3 +227,46 @@ func TestSanitizeIPs(t *testing.T) {
 		})
 	}
 }
+
+func TestReloader(t *testing.T) {
+	t.Run("updates the output configuration on the beat", func(t *testing.T) {
+		b, err := NewBeat("testbeat", "testidx", "0.9", false)
+		require.NoError(t, err)
+
+		cfg := `
+elasticsearch:
+  hosts: ["https://127.0.0.1:9200"]
+  username: "elastic"
+  allow_older_versions: true
+`
+		c, err := config.NewConfigWithYAML([]byte(cfg), cfg)
+		require.NoError(t, err)
+		outCfg, err := c.Child("elasticsearch", -1)
+		require.NoError(t, err)
+
+		update := &reload.ConfigWithMeta{Config: c}
+		m := &outputReloaderMock{}
+		reloader := b.makeOutputReloader(m)
+
+		require.False(t, b.Config.Output.IsSet(), "the output should not be set yet")
+		require.False(t, b.isConnectionToOlderVersionAllowed(), "the flag should not be present in the empty configuration")
+		err = reloader.Reload(update)
+		require.NoError(t, err)
+		require.True(t, b.Config.Output.IsSet(), "now the output should be set")
+		require.Equal(t, outCfg, b.Config.Output.Config())
+		require.Same(t, c, m.cfg.Config)
+		require.True(t, b.isConnectionToOlderVersionAllowed(), "the flag should be present")
+	})
+}
+
+type outputReloaderMock struct {
+	cfg *reload.ConfigWithMeta
+}
+
+func (r *outputReloaderMock) Reload(
+	cfg *reload.ConfigWithMeta,
+	factory func(o outputs.Observer, cfg config.Namespace) (outputs.Group, error),
+) error {
+	r.cfg = cfg
+	return nil
+}