diff --git a/ee/agent/types/registration.go b/ee/agent/types/registration.go
index e6563e195..1c39ef1f7 100644
--- a/ee/agent/types/registration.go
+++ b/ee/agent/types/registration.go
@@ -11,4 +11,3 @@ type RegistrationTracker interface {
 	RegistrationIDs() []string
 	SetRegistrationIDs(registrationIDs []string) error
 }
- 
\ No newline at end of file
diff --git a/pkg/osquery/runtime/runner.go b/pkg/osquery/runtime/runner.go
index 424bdd524..94b3c996c 100644
--- a/pkg/osquery/runtime/runner.go
+++ b/pkg/osquery/runtime/runner.go
@@ -7,6 +7,7 @@ import (
 	"log/slog"
 	"slices"
 	"sync"
+	"sync/atomic"
 	"time"
 
 	"github.com/kolide/launcher/ee/agent/flags/keys"
@@ -27,9 +28,9 @@ type Runner struct {
 	knapsack        types.Knapsack
 	serviceClient   service.KolideService   // shared service client for communication between osquery instance and Kolide SaaS
 	opts            []OsqueryInstanceOption // global options applying to all osquery instances
-	shutdown        chan struct{}
-	rerunRequired   bool
-	interrupted     bool
+	shutdown        chan struct{}           // buffered shutdown channel for to enable shutting down to restart or exit
+	rerunRequired   atomic.Bool
+	interrupted     atomic.Bool
 }
 
 func New(k types.Knapsack, serviceClient service.KolideService, opts ...OsqueryInstanceOption) *Runner {
@@ -39,9 +40,9 @@ func New(k types.Knapsack, serviceClient service.KolideService, opts ...OsqueryI
 		slogger:         k.Slogger().With("component", "osquery_runner"),
 		knapsack:        k,
 		serviceClient:   serviceClient,
-		shutdown:        make(chan struct{}),
-		rerunRequired:   false,
-		opts:            opts,
+		// the buffer length is arbitrarily set at 100, this number just needs to be higher than the total possible instances
+		shutdown: make(chan struct{}, 100),
+		opts:     opts,
 	}
 
 	k.RegisterChangeObserver(runner,
@@ -60,8 +61,8 @@ func (r *Runner) Run() error {
 
 		// if we're in a state that required re-running all registered instances,
 		// reset the field and do that
-		if r.rerunRequired {
-			r.rerunRequired = false
+		if r.rerunRequired.Load() {
+			r.rerunRequired.Store(false)
 			continue
 		}
 
@@ -214,6 +215,13 @@ func (r *Runner) Query(query string) ([]map[string]string, error) {
 }
 
 func (r *Runner) Interrupt(_ error) {
+	if r.interrupted.Load() {
+		// Already shut down, nothing else to do
+		return
+	}
+
+	r.interrupted.Store(true)
+
 	if err := r.Shutdown(); err != nil {
 		r.slogger.Log(context.TODO(), slog.LevelWarn,
 			"could not shut down runner on interrupt",
@@ -225,13 +233,12 @@ func (r *Runner) Interrupt(_ error) {
 // Shutdown instructs the runner to permanently stop the running instance (no
 // restart will be attempted).
 func (r *Runner) Shutdown() error {
-	if r.interrupted {
-		// Already shut down, nothing else to do
-		return nil
+	// ensure one shutdown is sent for each instance to read
+	r.instanceLock.Lock()
+	for range r.instances {
+		r.shutdown <- struct{}{}
 	}
-
-	r.interrupted = true
-	close(r.shutdown)
+	r.instanceLock.Unlock()
 
 	if err := r.triggerShutdownForInstances(); err != nil {
 		return fmt.Errorf("triggering shutdown for instances during runner shutdown: %w", err)
@@ -385,7 +392,7 @@ func (r *Runner) UpdateRegistrationIDs(newRegistrationIDs []string) error {
 	r.registrationIds = newRegistrationIDs
 	// mark rerun as required so that we can safely shutdown all workers and have the changes
 	// picked back up from within the main Run function
-	r.rerunRequired = true
+	r.rerunRequired.Store(true)
 
 	if err := r.Shutdown(); err != nil {
 		r.slogger.Log(context.TODO(), slog.LevelWarn,
@@ -396,9 +403,5 @@ func (r *Runner) UpdateRegistrationIDs(newRegistrationIDs []string) error {
 		return err
 	}
 
-	// reset the shutdown channel and interrupted state
-	r.shutdown = make(chan struct{})
-	r.interrupted = false
-
 	return nil
 }
diff --git a/pkg/osquery/runtime/runtime_test.go b/pkg/osquery/runtime/runtime_test.go
index 8b61d1e46..eb8a8fa17 100644
--- a/pkg/osquery/runtime/runtime_test.go
+++ b/pkg/osquery/runtime/runtime_test.go
@@ -638,11 +638,12 @@ func TestMultipleInstancesWithUpdatedRegistrationIDs(t *testing.T) {
 
 	// Add in an extra instance
 	extraRegistrationId := ulid.New()
-	runner.UpdateRegistrationIDs([]string{types.DefaultRegistrationID, extraRegistrationId})
+	updateErr := runner.UpdateRegistrationIDs([]string{types.DefaultRegistrationID, extraRegistrationId})
+	require.NoError(t, updateErr)
 	waitHealthy(t, runner, logBytes)
 	updatedInstanceStatuses := runner.InstanceStatuses()
 	// verify that rerunRequired has been reset for any future changes
-	require.False(t, runner.rerunRequired)
+	require.False(t, runner.rerunRequired.Load())
 	// now verify both instances are reported
 	require.Equal(t, 2, len(runner.instances))
 	require.Contains(t, updatedInstanceStatuses, types.DefaultRegistrationID)
@@ -655,7 +656,8 @@ func TestMultipleInstancesWithUpdatedRegistrationIDs(t *testing.T) {
 
 	// update registration IDs one more time, this time removing the additional registration
 	originalDefaultInstanceStartTime := runner.instances[extraRegistrationId].stats.StartTime
-	runner.UpdateRegistrationIDs([]string{types.DefaultRegistrationID})
+	updateErr = runner.UpdateRegistrationIDs([]string{types.DefaultRegistrationID})
+	require.NoError(t, updateErr)
 	waitHealthy(t, runner, logBytes)
 
 	// now verify only the default instance remains
@@ -666,7 +668,7 @@ func TestMultipleInstancesWithUpdatedRegistrationIDs(t *testing.T) {
 	require.NotEmpty(t, runner.instances[types.DefaultRegistrationID].stats.StartTime, "start time should be added to default instance stats on start up")
 	require.NotEmpty(t, runner.instances[types.DefaultRegistrationID].stats.ConnectTime, "connect time should be added to default instance stats on start up")
 	// verify that rerunRequired has been reset for any future changes
-	require.False(t, runner.rerunRequired)
+	require.False(t, runner.rerunRequired.Load())
 	// verify the default instance was restarted
 	require.NotEqual(t, originalDefaultInstanceStartTime, runner.instances[types.DefaultRegistrationID].stats.StartTime)
 
@@ -726,7 +728,8 @@ func TestUpdatingRegistrationIDsOnlyRestartsForChanges(t *testing.T) {
 	extraInstanceStartTime := runner.instances[extraRegistrationId].stats.StartTime
 
 	// rerun with identical registrationIDs in swapped order and verify that the instances are not restarted
-	runner.UpdateRegistrationIDs([]string{extraRegistrationId, types.DefaultRegistrationID})
+	updateErr := runner.UpdateRegistrationIDs([]string{extraRegistrationId, types.DefaultRegistrationID})
+	require.NoError(t, updateErr)
 	waitHealthy(t, runner, logBytes)
 
 	require.Equal(t, 2, len(runner.instances))