diff --git a/changelog/fragments/1666611696-fix_service_stop_timeout.yaml b/changelog/fragments/1666611696-fix_service_stop_timeout.yaml
new file mode 100644
index 00000000000..5125282618f
--- /dev/null
+++ b/changelog/fragments/1666611696-fix_service_stop_timeout.yaml
@@ -0,0 +1,4 @@
+kind: bug-fix
+summary: "Fix: Windows Agent Left Unhealthy After Removing Endpoint Integration"
+pr: 1286
+issue: 1262
diff --git a/internal/pkg/agent/operation/monitoring.go b/internal/pkg/agent/operation/monitoring.go
index f28c681e42a..d3f120da677 100644
--- a/internal/pkg/agent/operation/monitoring.go
+++ b/internal/pkg/agent/operation/monitoring.go
@@ -373,6 +373,7 @@ func (o *Operator) getMonitoringMetricbeatConfig(outputType string, output inter
 	if len(hosts) == 0 {
 		return nil, false
 	}
+	//nolint:prealloc // false positive
 	var modules []interface{}
 	fixedAgentName := strings.ReplaceAll(agentName, "-", "_")
 
@@ -668,7 +669,7 @@ func normalizeHTTPCopyRules(name string) []map[string]interface{} {
 		return fromToMap
 	}
 
-	for _, exportedMetric := range spec.ExprtedMetrics {
+	for _, exportedMetric := range spec.ExportedMetrics {
 		fromToMap = append(fromToMap, map[string]interface{}{
 			"from": fmt.Sprintf("http.agent.%s", exportedMetric),
 			"to":   exportedMetric,
diff --git a/internal/pkg/agent/operation/monitoring_test.go b/internal/pkg/agent/operation/monitoring_test.go
index 06a9cfbe23b..55b18741dad 100644
--- a/internal/pkg/agent/operation/monitoring_test.go
+++ b/internal/pkg/agent/operation/monitoring_test.go
@@ -37,7 +37,7 @@ import (
 func TestExportedMetrics(t *testing.T) {
 	programName := "testing"
 	expectedMetricsName := "metric_name"
-	program.SupportedMap[programName] = program.Spec{ExprtedMetrics: []string{expectedMetricsName}}
+	program.SupportedMap[programName] = program.Spec{ExportedMetrics: []string{expectedMetricsName}}
 
 	exportedMetrics := normalizeHTTPCopyRules(programName)
 
diff --git a/internal/pkg/agent/program/spec.go b/internal/pkg/agent/program/spec.go
index 12f860a1e9a..ead15104b31 100644
--- a/internal/pkg/agent/program/spec.go
+++ b/internal/pkg/agent/program/spec.go
@@ -8,6 +8,7 @@ import (
 	"fmt"
 	"io/ioutil"
 	"path/filepath"
+	"time"
 
 	"gopkg.in/yaml.v2"
 
@@ -40,11 +41,25 @@ type Spec struct {
 	When                  string               `yaml:"when"`
 	Constraints           string               `yaml:"constraints"`
 	RestartOnOutputChange bool                 `yaml:"restart_on_output_change,omitempty"`
-	ExprtedMetrics        []string             `yaml:"exported_metrics,omitempty"`
+	ExportedMetrics       []string             `yaml:"exported_metrics,omitempty"`
+	Process               *ProcessSettings     `yaml:"process,omitempty"`
+}
+
+// ProcessSettings process specific settings
+type ProcessSettings struct {
+	// Allows to override the agent stop timeout settings and specify a different stop timeout for Endpoint service
+	StopTimeout time.Duration `yaml:"stop_timeout"`
+}
+
+// Service info
+type ServiceInfo struct {
+	Name  string `yaml:"name"`
+	Label string `yaml:"label"`
 }
 
 // ReadSpecs reads all the specs that match the provided globbing path.
 func ReadSpecs(path string) ([]Spec, error) {
+	//nolint:prealloc // false positive
 	var specs []Spec
 	files, err := filepath.Glob(path)
 	if err != nil {
diff --git a/internal/pkg/agent/program/spec_test.go b/internal/pkg/agent/program/spec_test.go
index 110dd92eb36..2a3b5ec6048 100644
--- a/internal/pkg/agent/program/spec_test.go
+++ b/internal/pkg/agent/program/spec_test.go
@@ -5,13 +5,16 @@
 package program
 
 import (
+	"fmt"
 	"io/ioutil"
 	"os"
 	"path/filepath"
 	"regexp"
 	"strings"
 	"testing"
+	"time"
 
+	"github.com/google/go-cmp/cmp"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 	"gopkg.in/yaml.v2"
@@ -143,7 +146,48 @@ func TestExport(t *testing.T) {
 	for _, spec := range Supported {
 		b, err := yaml.Marshal(spec)
 		require.NoError(t, err)
-		err = ioutil.WriteFile(filepath.Join(dir, strings.ToLower(spec.Name)+".yml"), b, 0666)
+		err = ioutil.WriteFile(filepath.Join(dir, strings.ToLower(spec.Name)+".yml"), b, 0600)
 		require.NoError(t, err)
 	}
 }
+
+func TestSerializationProcessSettings(t *testing.T) {
+	ymlTmpl := `name: "Foobar"
+process:
+    stop_timeout: %v`
+
+	tests := []struct {
+		name  string
+		tonum int
+		to    time.Duration
+	}{
+		{"zero", 0, 0},
+		{"180ns", 180, 0},
+		{"180s", 0, 120 * time.Second},
+		{"3m", 0, 3 * time.Minute},
+	}
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			var (
+				yml         string
+				wantTimeout time.Duration
+			)
+			if tc.to == 0 {
+				yml = fmt.Sprintf(ymlTmpl, tc.tonum)
+				wantTimeout = time.Duration(tc.tonum)
+			} else {
+				yml = fmt.Sprintf(ymlTmpl, tc.to)
+				wantTimeout = tc.to
+			}
+			var spec Spec
+			err := yaml.Unmarshal([]byte(yml), &spec)
+			if err != nil {
+				t.Fatal(err)
+			}
+			diff := cmp.Diff(wantTimeout, spec.Process.StopTimeout)
+			if diff != "" {
+				t.Fatal(diff)
+			}
+		})
+	}
+}
diff --git a/internal/pkg/agent/program/supported.go b/internal/pkg/agent/program/supported.go
index 985ebb03709..690da9244fa 100644
--- a/internal/pkg/agent/program/supported.go
+++ b/internal/pkg/agent/program/supported.go
@@ -27,7 +27,7 @@ func init() {
 	// internal/spec/metricbeat.yml
 	// internal/spec/osquerybeat.yml
 	// internal/spec/packetbeat.yml
-	unpacked := packer.MustUnpack("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")
+	unpacked := packer.MustUnpack("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")
 	SupportedMap = make(map[string]Spec)
 
 	for f, v := range unpacked {
diff --git a/internal/pkg/core/plugin/service/app.go b/internal/pkg/core/plugin/service/app.go
index 312ac8b592e..af553ac5ac8 100644
--- a/internal/pkg/core/plugin/service/app.go
+++ b/internal/pkg/core/plugin/service/app.go
@@ -165,8 +165,8 @@ func (a *Application) Start(ctx context.Context, _ app.Taggable, cfg map[string]
 	// already started
 	if a.srvState != nil {
 		a.setState(state.Starting, "Starting", nil)
-		a.srvState.SetStatus(proto.StateObserved_STARTING, a.state.Message, a.state.Payload)
-		a.srvState.UpdateConfig(a.srvState.Config())
+		_ = a.srvState.SetStatus(proto.StateObserved_STARTING, a.state.Message, a.state.Payload)
+		_ = a.srvState.UpdateConfig(a.srvState.Config())
 	} else {
 		a.setState(state.Starting, "Starting", nil)
 		a.srvState, err = a.srv.Register(a, string(cfgStr))
@@ -247,6 +247,13 @@ func (a *Application) Configure(ctx context.Context, config map[string]interface
 	return err
 }
 
+func (a *Application) getStopTimeout() time.Duration {
+	if a.desc.Spec().Process != nil && a.desc.Spec().Process.StopTimeout > 0 {
+		return a.desc.Spec().Process.StopTimeout
+	}
+	return a.processConfig.StopTimeout
+}
+
 // Stop stops the current application.
 func (a *Application) Stop() {
 	a.appLock.Lock()
@@ -257,21 +264,36 @@ func (a *Application) Stop() {
 		return
 	}
 
-	if err := srvState.Stop(a.processConfig.StopTimeout); err != nil {
-		a.appLock.Lock()
-		a.setState(
-			state.Failed,
-			fmt.Errorf("failed to stop after %s: %w", a.processConfig.StopTimeout, err).Error(),
-			nil)
-	} else {
-		a.appLock.Lock()
-		a.setState(state.Stopped, "Stopped", nil)
+	name := a.desc.Spec().Name
+	to := a.getStopTimeout()
+
+	a.logger.Infof("Stop %v service, with %v timeout", name, to)
+	start := time.Now()
+
+	// Try to stop the service with timeout
+	// If timed out and the service is still not stopped the runtime is set to STOPPED state anyways.
+	// This avoids leaving the runtime indefinitely in the failed state.
+	//
+	// The Agent is not managing the Endpoint service state by design.
+	// The service runtime should send STOPPING state to the Endpoint service only before the Endpoint is expected to be uninstalled.
+	// So if the Agent never receives the STOPPING check-in from the Endpoint after this, it's ok to set the state
+	// to STOPPED following with the Endpoint service uninstall.
+	if err := srvState.Stop(to); err != nil {
+		// Log the error
+		a.logger.Errorf("Failed to stop %v service after %v timeout", name, to)
 	}
-	a.srvState = nil
 
+	// Cleanup
+	a.appLock.Lock()
+	defer a.appLock.Unlock()
+
+	a.srvState = nil
 	a.cleanUp()
 	a.stopCredsListener()
-	a.appLock.Unlock()
+
+	// Set the service state to "stopped", otherwise the agent is stuck in the failed stop state until restarted
+	a.logger.Infof("setting %s service status to Stopped, took: %v", name, time.Since(start))
+	a.setState(state.Stopped, "Stopped", nil)
 }
 
 // Shutdown disconnects the service, but doesn't signal it to stop.
@@ -327,7 +349,7 @@ func (a *Application) setState(s state.Status, msg string, payload map[string]in
 }
 
 func (a *Application) cleanUp() {
-	a.monitor.Cleanup(a.desc.Spec(), a.pipelineID)
+	_ = a.monitor.Cleanup(a.desc.Spec(), a.pipelineID)
 }
 
 func (a *Application) startCredsListener() error {
diff --git a/internal/spec/endpoint.yml b/internal/spec/endpoint.yml
index 5f452ba1943..e3e8c4fbe3e 100644
--- a/internal/spec/endpoint.yml
+++ b/internal/spec/endpoint.yml
@@ -2,6 +2,11 @@ name: Endpoint Security
 cmd: endpoint-security
 artifact: endpoint-dev
 service: 6788
+process:
+    # After discussion with Endpoint team the stop timeout is set to 3m,
+    # in order to give enough time for the Endpoint to stop gracefully.
+    # https://github.com/elastic/elastic-agent/issues/1262
+    stop_timeout: 3m
 action_input_types:
 - endpoint
 log_paths: