diff --git a/internal/beater/beater.go b/internal/beater/beater.go
index 7cb5c0310f..c6c2184347 100644
--- a/internal/beater/beater.go
+++ b/internal/beater/beater.go
@@ -410,6 +410,7 @@ func (s *Runner) Run(ctx context.Context) error {
 		kibanaClient,
 		newElasticsearchClient,
 		tracer,
+		s.logger,
 	)
 	if err != nil {
 		return err
diff --git a/internal/beater/beater_test.go b/internal/beater/beater_test.go
index 5a52994a6b..15cd3d5f32 100644
--- a/internal/beater/beater_test.go
+++ b/internal/beater/beater_test.go
@@ -37,6 +37,8 @@ import (
 	"github.com/stretchr/testify/require"
 	"go.elastic.co/apm/v2/apmtest"
 	"go.uber.org/zap"
+	"go.uber.org/zap/zapcore"
+	"go.uber.org/zap/zaptest/observer"
 
 	"github.com/elastic/apm-server/internal/beater/config"
 	"github.com/elastic/apm-server/internal/elasticsearch"
@@ -243,6 +245,28 @@ func TestRunnerNewDocappenderConfig(t *testing.T) {
 	}
 }
 
+func TestAgentConfigFetcherDeprecation(t *testing.T) {
+	core, observed := observer.New(zapcore.DebugLevel)
+	logger := logp.NewLogger("bo", zap.WrapCore(func(in zapcore.Core) zapcore.Core {
+		return zapcore.NewTee(in, core)
+	}))
+
+	_, _, err := newAgentConfigFetcher(context.Background(), &config.Config{
+		FleetAgentConfigs: []config.FleetAgentConfig{
+			{
+				AgentName: "foo",
+			},
+		},
+	}, nil, func(c *elasticsearch.Config) (*elasticsearch.Client, error) { return nil, nil }, nil, logger)
+	require.NoError(t, err)
+
+	all := observed.All()
+	assert.Len(t, all, 1)
+	record := all[0]
+	assert.Equal(t, zapcore.WarnLevel, record.Level, record.Message)
+	assert.Equal(t, agentcfgDeprecationNotice, record.Message)
+}
+
 func TestNewInstrumentation(t *testing.T) {
 	var auth string
 	labels := make(chan map[string]string, 1)
diff --git a/internal/beater/server.go b/internal/beater/server.go
index 973269cc8c..ac4593adee 100644
--- a/internal/beater/server.go
+++ b/internal/beater/server.go
@@ -49,6 +49,8 @@ import (
 
 var (
 	agentcfgMonitoringRegistry = monitoring.Default.NewRegistry("apm-server.agentcfg")
+
+	agentcfgDeprecationNotice = "deprecation notice: support for passing fleet agent configs will be removed in an upcoming version"
 )
 
 // WrapServerFunc is a function for injecting behaviour into ServerParams
@@ -240,6 +242,7 @@ func newAgentConfigFetcher(
 	kibanaClient *kibana.Client,
 	newElasticsearchClient func(*elasticsearch.Config) (*elasticsearch.Client, error),
 	tracer *apm.Tracer,
+	logger *logp.Logger,
 ) (agentcfg.Fetcher, func(context.Context) error, error) {
 	// Always use ElasticsearchFetcher, and as a fallback, use:
 	// 1. no fallback if Elasticsearch is explicitly configured
@@ -252,6 +255,7 @@ func newAgentConfigFetcher(
 	case cfg.AgentConfig.ESOverrideConfigured:
 		// Disable fallback because agent config Elasticsearch is explicitly configured.
 	case cfg.FleetAgentConfigs != nil:
+		logger.Warn(agentcfgDeprecationNotice)
 		agentConfigurations := agentcfg.ConvertAgentConfigs(cfg.FleetAgentConfigs)
 		fallbackFetcher = agentcfg.NewDirectFetcher(agentConfigurations)
 	case kibanaClient != nil: