diff --git a/.chloggen/fix_opamp-supervisor-bootstrap-error-shutdown.yaml b/.chloggen/fix_opamp-supervisor-bootstrap-error-shutdown.yaml
new file mode 100644
index 000000000000..dc6222b5577f
--- /dev/null
+++ b/.chloggen/fix_opamp-supervisor-bootstrap-error-shutdown.yaml
@@ -0,0 +1,13 @@
+# Use this changelog template to create an entry for release notes.
+
+# One of 'breaking', 'deprecation', 'new_component', 'enhancement', 'bug_fix'
+change_type: bug_fix
+
+# The name of the component, or a single word describing the area of concern, (e.g. filelogreceiver)
+component: cmd/opampsupervisor
+
+# A brief description of the change.  Surround your text with quotes ("") if it needs to start with a backtick (`).
+note: Fix collector subprocess not being stopped if bootstrapping fails
+
+# Mandatory: One or more tracking issues related to the change. You can use the PR number here if no issue exists.
+issues: [31943]
diff --git a/cmd/opampsupervisor/supervisor/supervisor.go b/cmd/opampsupervisor/supervisor/supervisor.go
index 87ad84ba543e..ca762660d86e 100644
--- a/cmd/opampsupervisor/supervisor/supervisor.go
+++ b/cmd/opampsupervisor/supervisor/supervisor.go
@@ -287,6 +287,12 @@ func (s *Supervisor) getBootstrapInfo() (err error) {
 		return err
 	}
 
+	defer func() {
+		if stopErr := srv.Stop(context.Background()); stopErr != nil {
+			err = errors.Join(err, fmt.Errorf("error when stopping the opamp server: %w", stopErr))
+		}
+	}()
+
 	cmd, err := commander.NewCommander(
 		s.logger,
 		s.config.Agent,
@@ -300,6 +306,12 @@ func (s *Supervisor) getBootstrapInfo() (err error) {
 		return err
 	}
 
+	defer func() {
+		if stopErr := cmd.Stop(context.Background()); stopErr != nil {
+			err = errors.Join(err, fmt.Errorf("error when stopping the collector: %w", stopErr))
+		}
+	}()
+
 	select {
 	// TODO make timeout configurable
 	case <-time.After(3 * time.Second):
@@ -309,20 +321,8 @@ func (s *Supervisor) getBootstrapInfo() (err error) {
 			return errors.New("collector's OpAMP client never connected to the Supervisor")
 		}
 	case err = <-done:
-		if err != nil {
-			return err
-		}
-	}
-
-	if err = cmd.Stop(context.Background()); err != nil {
-		return err
-	}
-
-	if err = srv.Stop(context.Background()); err != nil {
 		return err
 	}
-
-	return nil
 }
 
 func (s *Supervisor) Capabilities() protobufs.AgentCapabilities {