diff --git a/internal/pkg/agent/application/application.go b/internal/pkg/agent/application/application.go
index b6b47a30382..b312759b505 100644
--- a/internal/pkg/agent/application/application.go
+++ b/internal/pkg/agent/application/application.go
@@ -8,6 +8,7 @@ import (
 	"fmt"
 
 	"github.com/elastic/elastic-agent-libs/logp"
+	"github.com/elastic/elastic-agent/pkg/features"
 
 	"go.elastic.co/apm"
 
@@ -25,7 +26,6 @@ import (
 	"github.com/elastic/elastic-agent/pkg/component"
 	"github.com/elastic/elastic-agent/pkg/component/runtime"
 	"github.com/elastic/elastic-agent/pkg/core/logger"
-	"github.com/elastic/elastic-agent/pkg/features"
 )
 
 // New creates a new Agent and bootstrap the required subsystem.
@@ -38,40 +38,36 @@ func New(
 	tracer *apm.Tracer,
 	disableMonitoring bool,
 	modifiers ...component.PlatformModifier,
-) (*coordinator.Coordinator, error) {
+) (*coordinator.Coordinator, composable.Controller, error) {
 	platform, err := component.LoadPlatformDetail(modifiers...)
 	if err != nil {
-		return nil, fmt.Errorf("failed to gather system information: %w", err)
+		return nil, nil, fmt.Errorf("failed to gather system information: %w", err)
 	}
 	log.Info("Gathered system information")
 
 	specs, err := component.LoadRuntimeSpecs(paths.Components(), platform)
 	if err != nil {
-		return nil, fmt.Errorf("failed to detect inputs and outputs: %w", err)
+		return nil, nil, fmt.Errorf("failed to detect inputs and outputs: %w", err)
 	}
 	log.With("inputs", specs.Inputs()).Info("Detected available inputs and outputs")
 
 	caps, err := capabilities.Load(paths.AgentCapabilitiesPath(), log)
 	if err != nil {
-		return nil, fmt.Errorf("failed to determine capabilities: %w", err)
+		return nil, nil, fmt.Errorf("failed to determine capabilities: %w", err)
 	}
 	log.Info("Determined allowed capabilities")
 
 	pathConfigFile := paths.ConfigFile()
 	rawConfig, err := config.LoadFile(pathConfigFile)
 	if err != nil {
-		return nil, fmt.Errorf("failed to load configuration: %w", err)
+		return nil, nil, fmt.Errorf("failed to load configuration: %w", err)
 	}
 	if err := info.InjectAgentConfig(rawConfig); err != nil {
-		return nil, fmt.Errorf("failed to load configuration: %w", err)
+		return nil, nil, fmt.Errorf("failed to load configuration: %w", err)
 	}
 	cfg, err := configuration.NewFromConfig(rawConfig)
 	if err != nil {
-		return nil, fmt.Errorf("failed to load configuration: %w", err)
-	}
-
-	if err := features.Apply(rawConfig); err != nil {
-		return nil, fmt.Errorf("could not parse and apply feature flags config: %w", err)
+		return nil, nil, fmt.Errorf("failed to load configuration: %w", err)
 	}
 
 	// monitoring is not supported in bootstrap mode https://github.com/elastic/elastic-agent/issues/1761
@@ -89,7 +85,7 @@ func New(
 		cfg.Settings.GRPC,
 	)
 	if err != nil {
-		return nil, fmt.Errorf("failed to initialize runtime manager: %w", err)
+		return nil, nil, fmt.Errorf("failed to initialize runtime manager: %w", err)
 	}
 
 	var configMgr coordinator.ConfigManager
@@ -114,7 +110,7 @@ func New(
 		var store storage.Store
 		store, cfg, err = mergeFleetConfig(rawConfig)
 		if err != nil {
-			return nil, err
+			return nil, nil, err
 		}
 
 		if configuration.IsFleetServerBootstrap(cfg.Fleet) {
@@ -131,7 +127,7 @@ func New(
 
 			managed, err = newManagedConfigManager(log, agentInfo, cfg, store, runtime)
 			if err != nil {
-				return nil, err
+				return nil, nil, err
 			}
 			configMgr = managed
 		}
@@ -139,7 +135,7 @@ func New(
 
 	composable, err := composable.New(log, rawConfig, composableManaged)
 	if err != nil {
-		return nil, errors.New(err, "failed to initialize composable controller")
+		return nil, nil, errors.New(err, "failed to initialize composable controller")
 	}
 
 	coord := coordinator.New(log, logLevel, agentInfo, specs, reexec, upgrader, runtime, configMgr, composable, caps, monitor, isManaged, compModifiers...)
@@ -148,7 +144,14 @@ func New(
 		// coordinator, so it must be set here once the coordinator is created
 		managed.coord = coord
 	}
-	return coord, nil
+
+	// It is important that feature flags from configuration are applied as late as possible.  This will ensure that
+	// any feature flag change callbacks are registered before they get called by `features.Apply`.
+	if err := features.Apply(rawConfig); err != nil {
+		return nil, nil, fmt.Errorf("could not parse and apply feature flags config: %w", err)
+	}
+
+	return coord, composable, nil
 }
 
 func mergeFleetConfig(rawConfig *config.Config) (storage.Store, *configuration.Configuration, error) {
diff --git a/internal/pkg/agent/cmd/run.go b/internal/pkg/agent/cmd/run.go
index d6fa2127ef8..2d5d0ff4841 100644
--- a/internal/pkg/agent/cmd/run.go
+++ b/internal/pkg/agent/cmd/run.go
@@ -207,10 +207,11 @@ func run(override cfgOverrider, modifiers ...component.PlatformModifier) error {
 		l.Info("APM instrumentation disabled")
 	}
 
-	coord, err := application.New(l, baseLogger, logLvl, agentInfo, rex, tracer, configuration.IsFleetServerBootstrap(cfg.Fleet), modifiers...)
+	coord, composable, err := application.New(l, baseLogger, logLvl, agentInfo, rex, tracer, configuration.IsFleetServerBootstrap(cfg.Fleet), modifiers...)
 	if err != nil {
 		return err
 	}
+	defer composable.Close()
 
 	serverStopFn, err := setupMetrics(l, cfg.Settings.DownloadConfig.OS(), cfg.Settings.MonitoringConfig, tracer, coord)
 	if err != nil {
diff --git a/internal/pkg/agent/vars/vars.go b/internal/pkg/agent/vars/vars.go
index 65c0ef2ae1f..3a78b4e76f9 100644
--- a/internal/pkg/agent/vars/vars.go
+++ b/internal/pkg/agent/vars/vars.go
@@ -26,6 +26,7 @@ func WaitForVariables(ctx context.Context, l *logger.Logger, cfg *config.Config,
 	if err != nil {
 		return nil, fmt.Errorf("failed to create composable controller: %w", err)
 	}
+	defer composable.Close()
 
 	hasTimeout := false
 	if wait > time.Duration(0) {
diff --git a/internal/pkg/composable/controller.go b/internal/pkg/composable/controller.go
index 4c736bb7d0f..8c39dc4ed1e 100644
--- a/internal/pkg/composable/controller.go
+++ b/internal/pkg/composable/controller.go
@@ -34,6 +34,10 @@ type Controller interface {
 
 	// Watch returns the channel to watch for variable changes.
 	Watch() <-chan []*transpiler.Vars
+
+	// Close closes the controller, allowing for any resource
+	// cleanup and such.
+	Close()
 }
 
 // controller manages the state of the providers current context.
@@ -251,6 +255,34 @@ func (c *controller) Watch() <-chan []*transpiler.Vars {
 	return c.ch
 }
 
+// Close closes the controller, allowing for any resource
+// cleanup and such.
+func (c *controller) Close() {
+	// Attempt to close all closeable context providers.
+	for name, state := range c.contextProviders {
+		cp, ok := state.provider.(corecomp.CloseableProvider)
+		if !ok {
+			continue
+		}
+
+		if err := cp.Close(); err != nil {
+			c.logger.Errorf("unable to close context provider %q: %s", name, err.Error())
+		}
+	}
+
+	// Attempt to close all closeable dynamic providers.
+	for name, state := range c.dynamicProviders {
+		cp, ok := state.provider.(corecomp.CloseableProvider)
+		if !ok {
+			continue
+		}
+
+		if err := cp.Close(); err != nil {
+			c.logger.Errorf("unable to close dynamic provider %q: %s", name, err.Error())
+		}
+	}
+}
+
 type contextProviderState struct {
 	context.Context
 
diff --git a/internal/pkg/composable/controller_test.go b/internal/pkg/composable/controller_test.go
index 050fe78ed74..ec418795c19 100644
--- a/internal/pkg/composable/controller_test.go
+++ b/internal/pkg/composable/controller_test.go
@@ -191,6 +191,8 @@ func TestCancellation(t *testing.T) {
 		t.Run(fmt.Sprintf("test run %d", i), func(t *testing.T) {
 			c, err := composable.New(log, cfg, false)
 			require.NoError(t, err)
+			defer c.Close()
+
 			ctx, cancelFn := context.WithTimeout(context.Background(), timeout)
 			defer cancelFn()
 			err = c.Run(ctx)
@@ -205,6 +207,8 @@ func TestCancellation(t *testing.T) {
 	t.Run("immediate cancellation", func(t *testing.T) {
 		c, err := composable.New(log, cfg, false)
 		require.NoError(t, err)
+		defer c.Close()
+
 		ctx, cancelFn := context.WithTimeout(context.Background(), 0)
 		cancelFn()
 		err = c.Run(ctx)
diff --git a/internal/pkg/composable/providers/host/host.go b/internal/pkg/composable/providers/host/host.go
index ec7fef8927e..343d8d04488 100644
--- a/internal/pkg/composable/providers/host/host.go
+++ b/internal/pkg/composable/providers/host/host.go
@@ -20,8 +20,12 @@ import (
 	"github.com/elastic/elastic-agent/pkg/core/logger"
 )
 
-// DefaultCheckInterval is the default timeout used to check if any host information has changed.
-const DefaultCheckInterval = 5 * time.Minute
+const (
+	// DefaultCheckInterval is the default timeout used to check if any host information has changed.
+	DefaultCheckInterval = 5 * time.Minute
+
+	fqdnFeatureFlagCallbackID = "host_provider"
+)
 
 func init() {
 	composable.Providers.MustAddContextProvider("host", ContextProviderBuilder)
@@ -34,6 +38,10 @@ type contextProvider struct {
 
 	CheckInterval time.Duration `config:"check_interval"`
 
+	// fqdnFFChangeCh is used to signal when the FQDN
+	// feature flag has changed
+	fqdnFFChangeCh chan struct{}
+
 	// used by testing
 	fetcher infoFetcher
 }
@@ -49,21 +57,6 @@ func (c *contextProvider) Run(comm corecomp.ContextProviderComm) error {
 		return errors.New(err, "failed to set mapping", errors.TypeUnexpected)
 	}
 
-	const fqdnFeatureFlagCallbackID = "host_provider"
-	fqdnFFChangeCh := make(chan struct{})
-	err = features.AddFQDNOnChangeCallback(
-		onFQDNFeatureFlagChange(fqdnFFChangeCh),
-		fqdnFeatureFlagCallbackID,
-	)
-	if err != nil {
-		return fmt.Errorf("unable to add FQDN onChange callback in host provider: %w", err)
-	}
-
-	defer func() {
-		features.RemoveFQDNOnChangeCallback(fqdnFeatureFlagCallbackID)
-		close(fqdnFFChangeCh)
-	}()
-
 	// Update context when any host information changes.
 	for {
 		t := time.NewTimer(c.CheckInterval)
@@ -71,7 +64,7 @@ func (c *contextProvider) Run(comm corecomp.ContextProviderComm) error {
 		case <-comm.Done():
 			t.Stop()
 			return comm.Err()
-		case <-fqdnFFChangeCh:
+		case <-c.fqdnFFChangeCh:
 		case <-t.C:
 		}
 
@@ -92,13 +85,21 @@ func (c *contextProvider) Run(comm corecomp.ContextProviderComm) error {
 	}
 }
 
-func onFQDNFeatureFlagChange(fqdnFFChangeCh chan struct{}) features.BoolValueOnChangeCallback {
-	return func(new, old bool) {
-		// FQDN feature flag was toggled, so notify on channel
-		fqdnFFChangeCh <- struct{}{}
+func (c *contextProvider) onFQDNFeatureFlagChange(new, old bool) {
+	// FQDN feature flag was toggled, so notify on channel
+	select {
+	case c.fqdnFFChangeCh <- struct{}{}:
+	default:
 	}
 }
 
+func (c *contextProvider) Close() error {
+	features.RemoveFQDNOnChangeCallback(fqdnFeatureFlagCallbackID)
+	close(c.fqdnFFChangeCh)
+
+	return nil
+}
+
 // ContextProviderBuilder builds the context provider.
 func ContextProviderBuilder(log *logger.Logger, c *config.Config, _ bool) (corecomp.ContextProvider, error) {
 	p := &contextProvider{
@@ -114,6 +115,16 @@ func ContextProviderBuilder(log *logger.Logger, c *config.Config, _ bool) (corec
 	if p.CheckInterval <= 0 {
 		p.CheckInterval = DefaultCheckInterval
 	}
+
+	p.fqdnFFChangeCh = make(chan struct{}, 1)
+	err := features.AddFQDNOnChangeCallback(
+		p.onFQDNFeatureFlagChange,
+		fqdnFeatureFlagCallbackID,
+	)
+	if err != nil {
+		return nil, fmt.Errorf("unable to add FQDN onChange callback in host provider: %w", err)
+	}
+
 	return p, nil
 }
 
diff --git a/internal/pkg/composable/providers/host/host_test.go b/internal/pkg/composable/providers/host/host_test.go
index 62fb9738505..dbdd0ed08e7 100644
--- a/internal/pkg/composable/providers/host/host_test.go
+++ b/internal/pkg/composable/providers/host/host_test.go
@@ -101,6 +101,13 @@ func TestFQDNFeatureFlagToggle(t *testing.T) {
 	provider, err := builder(log, c, true)
 	require.NoError(t, err)
 
+	hostProvider, ok := provider.(*contextProvider)
+	require.True(t, ok)
+	defer func() {
+		err := hostProvider.Close()
+		require.NoError(t, err)
+	}()
+
 	ctx, cancel := context.WithCancel(context.Background())
 	defer func() {
 		cancel()
@@ -109,9 +116,6 @@ func TestFQDNFeatureFlagToggle(t *testing.T) {
 
 	// Track the number of times hostProvider.fetcher is called.
 	numCalled := 0
-	hostProvider, ok := provider.(*contextProvider)
-	require.True(t, ok)
-
 	hostProvider.fetcher = func() (map[string]interface{}, error) {
 		numCalled++
 		return nil, nil
@@ -119,16 +123,9 @@ func TestFQDNFeatureFlagToggle(t *testing.T) {
 
 	// Run the provider
 	go func() {
-		err = provider.Run(comm)
+		err = hostProvider.Run(comm)
 	}()
 
-	// Wait long enough for provider.Run to register
-	// the FQDN feature flag onChange callback.
-	numCallbacks := features.NumFQDNOnChangeCallbacks()
-	require.Eventually(t, func() bool {
-		return features.NumFQDNOnChangeCallbacks() == numCallbacks+1
-	}, 100*time.Millisecond, 10*time.Millisecond)
-
 	// Trigger the FQDN feature flag callback by
 	// toggling the FQDN feature flag
 	err = features.Apply(config.MustNewConfigFrom(map[string]interface{}{
@@ -143,7 +140,7 @@ func TestFQDNFeatureFlagToggle(t *testing.T) {
 		// - once, right after the provider is run, and
 		// - once again, when the FQDN feature flag callback is triggered
 		return numCalled == 2
-	}, 100*time.Millisecond, 10*time.Millisecond)
+	}, 10*time.Second, 100*time.Millisecond)
 }
 
 func returnHostMapping(log *logger.Logger) infoFetcher {
diff --git a/internal/pkg/core/composable/providers.go b/internal/pkg/core/composable/providers.go
index 235e17d83fa..f6d2a8f3e26 100644
--- a/internal/pkg/core/composable/providers.go
+++ b/internal/pkg/core/composable/providers.go
@@ -28,3 +28,11 @@ type ContextProvider interface {
 	// Run runs the context provider.
 	Run(ContextProviderComm) error
 }
+
+// CloseableProvider is an interface that providers may choose to implement
+// if it makes sense for them, e.g. if they have any resources that need
+// cleaning up after the provider's (final) run.
+type CloseableProvider interface {
+	// Close is called after all runs of the provider have finished.
+	Close() error
+}
diff --git a/pkg/features/features.go b/pkg/features/features.go
index 07b48877d87..7613b055fd2 100644
--- a/pkg/features/features.go
+++ b/pkg/features/features.go
@@ -81,15 +81,6 @@ func RemoveFQDNOnChangeCallback(id string) {
 	delete(current.fqdnCallbacks, id)
 }
 
-// NumFQDNOnChangeCallbacks returns the number of FQDN onChange
-// callbacks currently registered.  Useful for testing.
-func NumFQDNOnChangeCallbacks() int {
-	current.mu.RLock()
-	defer current.mu.RUnlock()
-
-	return len(current.fqdnCallbacks)
-}
-
 // setFQDN sets the value of the FQDN flag in Flags.
 func (f *Flags) setFQDN(newValue bool) {
 	f.mu.Lock()