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..41cf966aaed 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"
 
@@ -40,7 +41,20 @@ 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.
diff --git a/internal/pkg/agent/program/spec_test.go b/internal/pkg/agent/program/spec_test.go
index 110dd92eb36..31985d3d6d7 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"
@@ -147,3 +150,44 @@ func TestExport(t *testing.T) {
 		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 52685137b97..0938fbff351 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: