diff --git a/beater/beater.go b/beater/beater.go
index 02f172abc6a..501d36f341d 100644
--- a/beater/beater.go
+++ b/beater/beater.go
@@ -31,6 +31,7 @@ import (
 	"github.com/elastic/beats/v7/libbeat/beat"
 	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/common"
+	"github.com/elastic/beats/v7/libbeat/common/reload"
 	"github.com/elastic/beats/v7/libbeat/esleg/eslegclient"
 	"github.com/elastic/beats/v7/libbeat/instrumentation"
 	"github.com/elastic/beats/v7/libbeat/logp"
@@ -67,66 +68,43 @@ func NewCreator(args CreatorParams) beat.Creator {
 		if err := checkConfig(logger); err != nil {
 			return nil, err
 		}
-		var esOutputCfg *common.Config
-		if isElasticsearchOutput(b) {
-			esOutputCfg = b.Config.Output.Config()
+		bt := &beater{
+			rawConfig:     ucfg,
+			stopped:       false,
+			logger:        logger,
+			wrapRunServer: args.WrapRunServer,
 		}
 
-		beaterConfig, err := config.NewConfig(ucfg, esOutputCfg)
+		esOutputCfg := elasticsearchOutputConfig(b)
+
+		var err error
+		bt.config, err = config.NewConfig(bt.rawConfig, esOutputCfg)
 		if err != nil {
 			return nil, err
 		}
-		// send configs to telemetry
-		recordConfigs(b.Info, beaterConfig, ucfg, logger)
 
-		bt := &beater{
-			config:        beaterConfig,
-			stopped:       false,
-			logger:        logger,
-			wrapRunServer: args.WrapRunServer,
-		}
+		// setup pipelines if explicitly directed to or setup --pipelines and config is not set at all,
+		// and apm-server is not running supervised by Elastic Agent
+		shouldSetupPipelines := bt.config.Register.Ingest.Pipeline.IsEnabled() ||
+			(b.InSetupCmd && bt.config.Register.Ingest.Pipeline.Enabled == nil)
+		runningUnderElasticAgent := b.Manager != nil && b.Manager.Enabled()
 
-		// setup pipelines if explicitly directed to or setup --pipelines and config is not set at all
-		shouldSetupPipelines := beaterConfig.Register.Ingest.Pipeline.IsEnabled() ||
-			(b.InSetupCmd && beaterConfig.Register.Ingest.Pipeline.Enabled == nil)
-		if isElasticsearchOutput(b) && shouldSetupPipelines {
-			logger.Info("Registering pipeline callback")
+		if esOutputCfg != nil && shouldSetupPipelines && !runningUnderElasticAgent {
+			bt.logger.Info("Registering pipeline callback")
 			err := bt.registerPipelineCallback(b)
 			if err != nil {
 				return nil, err
 			}
 		} else {
-			logger.Info("No pipeline callback registered")
+			bt.logger.Info("No pipeline callback registered")
 		}
-		return bt, nil
-	}
-}
 
-// checkConfig verifies the global configuration doesn't use unsupported settings
-func checkConfig(logger *logp.Logger) error {
-	cfg, err := cfgfile.Load("", nil)
-	if err != nil {
-		// responsibility for failing to load configuration lies elsewhere
-		// this is not reachable after going through normal beat creation
-		return nil
-	}
-
-	var s struct {
-		Dashboards *common.Config `config:"setup.dashboards"`
-	}
-	if err := cfg.Unpack(&s); err != nil {
-		return err
-	}
-	if s.Dashboards != nil {
-		if s.Dashboards.Enabled() {
-			return errSetupDashboardRemoved
-		}
-		logger.Warn(errSetupDashboardRemoved)
+		return bt, nil
 	}
-	return nil
 }
 
 type beater struct {
+	rawConfig     *common.Config
 	config        *config.Config
 	logger        *logp.Logger
 	wrapRunServer func(RunServerFunc) RunServerFunc
@@ -140,6 +118,35 @@ type beater struct {
 // or a fatal error occurs.
 func (bt *beater) Run(b *beat.Beat) error {
 
+	done := make(chan struct{})
+
+	var reloadOnce sync.Once
+	var reloadable = reload.ReloadableFunc(func(ucfg *reload.ConfigWithMeta) error {
+		var err error
+		// Elastic Agent might call ReloadableFunc many times, but we only need to act upon the first call,
+		// during startup. This might change when APM Server is included in Fleet
+		reloadOnce.Do(func() {
+			defer close(done)
+			var cfg *config.Config
+			cfg, err = config.NewConfig(ucfg.Config, elasticsearchOutputConfig(b))
+			if err != nil {
+				bt.logger.Warn("Could not parse configuration from Elastic Agent ", err)
+			}
+			bt.config = cfg
+			bt.rawConfig = ucfg.Config
+			bt.logger.Info("Applying configuration from Elastic Agent... ")
+		})
+		return err
+	})
+	if b.Manager != nil && b.Manager.Enabled() {
+		bt.logger.Info("Running under Elastic Agent, waiting for configuration... ")
+		reload.Register.MustRegister("inputs", reloadable)
+		<-done
+	}
+
+	// send configs to telemetry
+	recordConfigs(b.Info, bt.config, bt.rawConfig, bt.logger)
+
 	tracer, tracerServer, err := bt.initTracing(b)
 	if err != nil {
 		return err
@@ -212,8 +219,36 @@ func (bt *beater) Run(b *beat.Beat) error {
 	})
 }
 
-func isElasticsearchOutput(b *beat.Beat) bool {
-	return b.Config != nil && b.Config.Output.Name() == "elasticsearch"
+// checkConfig verifies the global configuration doesn't use unsupported settings
+func checkConfig(logger *logp.Logger) error {
+	cfg, err := cfgfile.Load("", nil)
+	if err != nil {
+		// responsibility for failing to load configuration lies elsewhere
+		// this is not reachable after going through normal beat creation
+		return nil
+	}
+
+	var s struct {
+		Dashboards *common.Config `config:"setup.dashboards"`
+	}
+	if err := cfg.Unpack(&s); err != nil {
+		return err
+	}
+	if s.Dashboards != nil {
+		if s.Dashboards.Enabled() {
+			return errSetupDashboardRemoved
+		}
+		logger.Warn(errSetupDashboardRemoved)
+	}
+	return nil
+}
+
+// elasticsearchOutputConfig returns nil if the output is not elasticsearch
+func elasticsearchOutputConfig(b *beat.Beat) *common.Config {
+	if b.Config != nil && b.Config.Output.Name() == "elasticsearch" {
+		return b.Config.Output.Config()
+	}
+	return nil
 }
 
 func (bt *beater) registerPipelineCallback(b *beat.Beat) error {