diff --git a/go.mod b/go.mod
index 3f2ed7094917..c63ea27795cd 100644
--- a/go.mod
+++ b/go.mod
@@ -134,7 +134,7 @@ require (
 	golang.org/x/net v0.33.0
 	golang.org/x/oauth2 v0.22.0
 	golang.org/x/sync v0.10.0
-	golang.org/x/sys v0.28.0
+	golang.org/x/sys v0.29.0
 	golang.org/x/term v0.27.0
 	golang.org/x/text v0.21.0
 	golang.org/x/tools v0.23.0
@@ -197,6 +197,8 @@ require (
 	github.com/go-logr/logr v1.4.2 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
 	github.com/gobwas/glob v0.2.3 // indirect
+	github.com/godbus/dbus/v5 v5.1.0 // indirect
+	github.com/gofrs/flock v0.12.1 // indirect
 	github.com/gogo/protobuf v1.3.2 // indirect
 	github.com/golang/glog v1.2.4 // indirect
 	github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect
diff --git a/go.sum b/go.sum
index bcc3c180ff57..fdac1395c871 100644
--- a/go.sum
+++ b/go.sum
@@ -338,6 +338,8 @@ github.com/gocarina/gocsv v0.0.0-20220310154401-d4df709ca055/go.mod h1:5YoVOkjYA
 github.com/godbus/dbus/v5 v5.0.4/go.mod h1:xhWf0FNVPg57R7Z0UbKHbJfkEywrmjJnf7w5xrFpKfA=
 github.com/godbus/dbus/v5 v5.1.0 h1:4KLkAxT3aOY8Li4FRJe/KvhoNFFxo0m6fNuFUO8QJUk=
 github.com/godbus/dbus/v5 v5.1.0/go.mod h1:xhWf0FNVPg57R7Z0UbKHbJfkEywrmjJnf7w5xrFpKfA=
+github.com/gofrs/flock v0.12.1 h1:MTLVXXHf8ekldpJk3AKicLij9MdwOWkZ+a/jHHZby9E=
+github.com/gofrs/flock v0.12.1/go.mod h1:9zxTsyu5xtJ9DK+1tFZyibEV7y3uwDxPPfbxeeHCoD0=
 github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
 github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4=
 github.com/gogo/protobuf v1.3.2 h1:Ov1cvc58UF3b5XjBnZv7+opcTcQFZebYjWzi34vdm4Q=
@@ -1097,6 +1099,8 @@ golang.org/x/sys v0.12.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.18.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
 golang.org/x/sys v0.28.0 h1:Fksou7UEQUWlKvIdsqzJmUmCX3cZuD2+P3XyyzwMhlA=
 golang.org/x/sys v0.28.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
+golang.org/x/sys v0.29.0 h1:TPYlXGxvx1MGTn2GiZDhnjPA9wZzZeGKHHmKhHYvgaU=
+golang.org/x/sys v0.29.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
 golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
 golang.org/x/term v0.0.0-20210220032956-6a3ed077a48d/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
 golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
diff --git a/orbit/changes/25396-fleet-desktop-lockfile b/orbit/changes/25396-fleet-desktop-lockfile
new file mode 100644
index 000000000000..7662dcf6ba45
--- /dev/null
+++ b/orbit/changes/25396-fleet-desktop-lockfile
@@ -0,0 +1 @@
+- Ensure only one copy of fleet desktop is running at a time
diff --git a/orbit/cmd/desktop/desktop.go b/orbit/cmd/desktop/desktop.go
index ebb8800ce9b4..bb76e305fd32 100644
--- a/orbit/cmd/desktop/desktop.go
+++ b/orbit/cmd/desktop/desktop.go
@@ -25,6 +25,7 @@ import (
 	"github.com/fleetdm/fleet/v4/pkg/open"
 	"github.com/fleetdm/fleet/v4/server/fleet"
 	"github.com/fleetdm/fleet/v4/server/service"
+	"github.com/gofrs/flock"
 	"github.com/oklog/run"
 	"github.com/rs/zerolog"
 	"github.com/rs/zerolog/log"
@@ -110,6 +111,21 @@ func main() {
 		log.Info().Msgf("got a TUF update root: %s", tufUpdateRoot)
 	}
 
+	// We've only seen this bug appear on Linux under certain very
+	// specific conditions
+	if runtime.GOOS == "linux" {
+		// Ensure only one instance of Fleet Desktop is running at a time
+		lockFile, err := getLockfile()
+		if err != nil {
+			log.Fatal().Err(err).Msg("could not secure lock file")
+		}
+		defer func() {
+			if err := lockFile.Unlock(); err != nil {
+				log.Error().Err(err).Msg("unlocking lockfile")
+			}
+		}()
+	}
+
 	// Setting up working runners such as signalHandler runner
 	go setupRunners()
 
@@ -564,6 +580,32 @@ func (m *mdmMigrationHandler) ShowInstructions() error {
 	return nil
 }
 
+// getLockfile checks for the fleet desktop lock file, and returns an error if it can't secure it.
+func getLockfile() (*flock.Flock, error) {
+	dir, err := logDir()
+	if err != nil {
+		return nil, fmt.Errorf("unable to get logdir for lock: %w", err)
+	}
+	// Same as the log dir in setupLogs()
+	dir = filepath.Join(dir, "Fleet")
+
+	lockFilePath := filepath.Join(dir, "fleet-desktop.lock")
+	log.Debug().Msgf("acquiring fleet desktop lockfile: %s", lockFilePath)
+
+	lock := flock.New(lockFilePath)
+	locked, err := lock.TryLock()
+	if err != nil {
+		return nil, fmt.Errorf("error getting lock on %s: %w", lockFilePath, err)
+	}
+	if !locked {
+		return nil, errors.New("another instance of fleet desktop has the lock")
+	}
+
+	log.Debug().Msgf("lock acquired on %s", lockFilePath)
+
+	return lock, nil
+}
+
 // setupLogs configures our logging system to write logs to rolling files, if for some
 // reason we can't write a log file the logs are still printed to stderr.
 func setupLogs() {
diff --git a/orbit/cmd/orbit/orbit.go b/orbit/cmd/orbit/orbit.go
index 318f105f1949..802cf145a78b 100644
--- a/orbit/cmd/orbit/orbit.go
+++ b/orbit/cmd/orbit/orbit.go
@@ -1585,14 +1585,6 @@ func newDesktopRunner(
 func (d *desktopRunner) Execute() error {
 	defer close(d.executeDoneCh)
 
-	log.Info().Msg("killing any pre-existing fleet-desktop instances")
-
-	if err := platform.SignalProcessBeforeTerminate(constant.DesktopAppExecName); err != nil &&
-		!errors.Is(err, platform.ErrProcessNotFound) &&
-		!errors.Is(err, platform.ErrComChannelNotFound) {
-		log.Error().Err(err).Msg("desktop early terminate")
-	}
-
 	log.Info().Str("path", d.desktopPath).Msg("opening")
 	url, err := url.Parse(d.fleetURL)
 	if err != nil {
@@ -1640,6 +1632,13 @@ func (d *desktopRunner) Execute() error {
 				return true
 			}
 
+			log.Info().Msg("killing any pre-existing fleet-desktop instances")
+			if err := platform.SignalProcessBeforeTerminate(constant.DesktopAppExecName); err != nil &&
+				!errors.Is(err, platform.ErrProcessNotFound) &&
+				!errors.Is(err, platform.ErrComChannelNotFound) {
+				log.Error().Err(err).Msg("desktop early terminate")
+			}
+
 			// Orbit runs as root user on Unix and as SYSTEM (Windows Service) user on Windows.
 			// To be able to run the desktop application (mostly to register the icon in the system tray)
 			// we need to run the application as the login user.
@@ -1657,7 +1656,7 @@ func (d *desktopRunner) Execute() error {
 		// Second retry logic to monitor fleet-desktop.
 		// Call with waitFirst=true to give some time for the process to start.
 		if done := retry(15*time.Second, true, d.interruptCh, func() bool {
-			switch _, err := platform.GetProcessByName(constant.DesktopAppExecName); {
+			switch _, err := platform.GetProcessesByName(constant.DesktopAppExecName); {
 			case err == nil:
 				return true // all good, process is running, retry.
 			case errors.Is(err, platform.ErrProcessNotFound):
diff --git a/orbit/pkg/platform/platform.go b/orbit/pkg/platform/platform.go
index eb1f894811ed..af07c59a84f3 100644
--- a/orbit/pkg/platform/platform.go
+++ b/orbit/pkg/platform/platform.go
@@ -27,13 +27,15 @@ func killProcessByName(name string) error {
 		return errors.New("process name should not be empty")
 	}
 
-	foundProcess, err := GetProcessByName(name)
+	foundProcesses, err := GetProcessesByName(name)
 	if err != nil {
 		return fmt.Errorf("get process: %w", err)
 	}
 
-	if err := foundProcess.Kill(); err != nil {
-		return fmt.Errorf("kill process %d: %w", foundProcess.Pid, err)
+	for _, foundProcess := range foundProcesses {
+		if err := foundProcess.Kill(); err != nil {
+			return fmt.Errorf("kill process %d: %w", foundProcess.Pid, err)
+		}
 	}
 
 	return nil
diff --git a/orbit/pkg/platform/platform_notwindows.go b/orbit/pkg/platform/platform_notwindows.go
index 930e6dc28a30..d3c442c2a4e3 100644
--- a/orbit/pkg/platform/platform_notwindows.go
+++ b/orbit/pkg/platform/platform_notwindows.go
@@ -54,9 +54,9 @@ func SignalProcessBeforeTerminate(processName string) error {
 	return nil
 }
 
-// GetProcessByName gets a single running process object by its name.
+// GetProcessesByName gets all running processes by its name.
 // Returns ErrProcessNotFound if the process was not found running.
-func GetProcessByName(name string) (*gopsutil_process.Process, error) {
+func GetProcessesByName(name string) ([]*gopsutil_process.Process, error) {
 	if name == "" {
 		return nil, errors.New("process name should not be empty")
 	}
@@ -66,7 +66,7 @@ func GetProcessByName(name string) (*gopsutil_process.Process, error) {
 		return nil, err
 	}
 
-	var foundProcess *gopsutil_process.Process
+	var foundProcesses []*gopsutil_process.Process
 	for _, process := range processes {
 		processName, err := process.Name()
 		if err != nil {
@@ -75,16 +75,16 @@ func GetProcessByName(name string) (*gopsutil_process.Process, error) {
 		}
 
 		if strings.HasPrefix(processName, name) {
-			foundProcess = process
+			foundProcesses = append(foundProcesses, process)
 			break
 		}
 	}
 
-	if foundProcess == nil {
+	if len(foundProcesses) == 0 {
 		return nil, ErrProcessNotFound
 	}
 
-	return foundProcess, nil
+	return foundProcesses, nil
 }
 
 func GetSMBiosUUID() (string, UUIDSource, error) {
diff --git a/orbit/pkg/platform/platform_windows.go b/orbit/pkg/platform/platform_windows.go
index a0fc336b0788..03a82ed5d64d 100644
--- a/orbit/pkg/platform/platform_windows.go
+++ b/orbit/pkg/platform/platform_windows.go
@@ -131,20 +131,23 @@ func SignalProcessBeforeTerminate(processName string) error {
 		return ErrComChannelNotFound
 	}
 
-	foundProcess, err := GetProcessByName(processName)
+	foundProcesses, err := GetProcessesByName(processName)
 	if err != nil {
 		return fmt.Errorf("get process: %w", err)
 	}
 
-	if err := foundProcess.Kill(); err != nil {
-		return fmt.Errorf("kill process %d: %w", foundProcess.Pid, err)
+	for _, foundProcess := range foundProcesses {
+		if err := foundProcess.Kill(); err != nil {
+			return fmt.Errorf("kill process %d: %w", foundProcess.Pid, err)
+		}
 	}
+
 	return nil
 }
 
-// GetProcessByName gets a single running process object by its name.
+// GetProcessesByName returns a list of running process object by name.
 // Returns ErrProcessNotFound if the process was not found running.
-func GetProcessByName(name string) (*gopsutil_process.Process, error) {
+func GetProcessesByName(name string) ([]*gopsutil_process.Process, error) {
 	if name == "" {
 		return nil, errors.New("process name should not be empty")
 	}
@@ -164,7 +167,7 @@ func GetProcessByName(name string) (*gopsutil_process.Process, error) {
 	// Closing the handle to avoid handle leaks.
 	defer windows.CloseHandle(snapshot) //nolint:errcheck
 
-	var foundProcessID uint32 = 0
+	var foundProcessIDs []uint32
 
 	// Initializing work structure PROCESSENTRY32W
 	// https://learn.microsoft.com/en-us/windows/win32/api/tlhelp32/ns-tlhelp32-processentry32w
@@ -180,10 +183,8 @@ func GetProcessByName(name string) (*gopsutil_process.Process, error) {
 	// Process32First() is going to return ERROR_NO_MORE_FILES when no more threads present
 	// it will return FALSE/nil otherwise
 	for err == nil {
-
 		if strings.HasPrefix(syscall.UTF16ToString(procEntry.ExeFile[:]), name) {
-			foundProcessID = procEntry.ProcessID
-			break
+			foundProcessIDs = append(foundProcessIDs, procEntry.ProcessID)
 		}
 
 		// Process32Next() is calling to keep iterating the snapshot
@@ -191,17 +192,27 @@ func GetProcessByName(name string) (*gopsutil_process.Process, error) {
 		err = windows.Process32Next(snapshot, &procEntry)
 	}
 
-	process, err := gopsutil_process.NewProcess(int32(foundProcessID))
-	if err != nil {
-		return nil, fmt.Errorf("NewProcess: %w", err)
+	var processes []*gopsutil_process.Process
+
+	for _, foundProcessID := range foundProcessIDs {
+		process, err := gopsutil_process.NewProcess(int32(foundProcessID))
+		if err != nil {
+			continue
+		}
+
+		isRunning, err := process.IsRunning()
+		if err != nil || !isRunning {
+			continue
+		}
+
+		processes = append(processes, process)
 	}
 
-	isRunning, err := process.IsRunning()
-	if err != nil || !isRunning {
+	if len(processes) == 0 {
 		return nil, ErrProcessNotFound
 	}
 
-	return process, nil
+	return processes, nil
 }
 
 // It obtains the BIOS UUID by calling "cmd.exe /c wmic csproduct get UUID" and parsing the results
diff --git a/pkg/open/open_linux.go b/pkg/open/open_linux.go
index b68c704d19e1..a84d6f8bf1b9 100644
--- a/pkg/open/open_linux.go
+++ b/pkg/open/open_linux.go
@@ -41,18 +41,18 @@ func browser(url string) error {
 // getXWaylandAuthority retrieves the X authority file path from
 // the running XWayland process environment.
 func getXWaylandAuthority() (xAuthorityPath string, err error) {
-	xWaylandProcess, err := platform.GetProcessByName("Xwayland")
+	xWaylandProcess, err := platform.GetProcessesByName("Xwayland")
 	if err != nil {
 		return "", fmt.Errorf("get process by name: %w", err)
 	}
-	executablePath, err := xWaylandProcess.Exe()
+	executablePath, err := xWaylandProcess[0].Exe()
 	if err != nil {
 		return "", fmt.Errorf("get executable path: %w", err)
 	}
 	if executablePath != "/usr/bin/Xwayland" {
 		return "", fmt.Errorf("invalid Xwayland path: %q", executablePath)
 	}
-	envs, err := xWaylandProcess.Environ()
+	envs, err := xWaylandProcess[0].Environ()
 	if err != nil {
 		return "", fmt.Errorf("get environment: %w", err)
 	}