diff --git a/README.md b/README.md
index bd53a9f..589b862 100644
--- a/README.md
+++ b/README.md
@@ -274,6 +274,7 @@ Standard 5-field cron schedules:
 Changing `jobs_dir` saves the current job list to the new directory.
 
 The `Start on login` setting shows an `OK` or `Problem` status next to the checkbox. Saving settings with the checkbox enabled rewrites the autostart entry using the current executable path.
+Autostart entries add `--start-in-tray`, so scheduled jobs begin running after sign-in without opening the main window.
 
 ## Autostart
 
@@ -292,7 +293,7 @@ Linux:
 [Desktop Entry]
 Type=Application
 Name=PySentry
-Exec=/opt/pysentry/pysentry-0.2.4-linux-amd64
+Exec=/opt/pysentry/pysentry-0.2.4-linux-amd64 --start-in-tray
 Terminal=false
 ```
 
@@ -301,8 +302,9 @@ Windows:
 ```text
 # PySentry writes a shortcut to the current user's Startup folder when Start on
 # login is enabled. A .lnk stores the executable path as a structured TargetPath,
-# so paths with spaces do not need fragile command-line quoting. Saving settings
-# rewrites the shortcut and removes old HKCU Run entries from earlier builds.
+# and stores --start-in-tray as Arguments, so paths with spaces do not need
+# fragile command-line quoting. Saving settings rewrites the shortcut and removes
+# old HKCU Run entries from earlier builds.
 %APPDATA%\Microsoft\Windows\Start Menu\Programs\Startup\GoSentry.lnk
 ```
 
diff --git a/cmd/pysentry/main.go b/cmd/pysentry/main.go
index 7fc550c..c318839 100644
--- a/cmd/pysentry/main.go
+++ b/cmd/pysentry/main.go
@@ -1,10 +1,24 @@
 package main
 
-import "github.com/pysentry/pysentry/src/gui"
+import (
+	"os"
+
+	"github.com/pysentry/pysentry/src/core"
+	"github.com/pysentry/pysentry/src/gui"
+)
 
 func main() {
 	// The executable entry point intentionally delegates all startup work to the
 	// GUI package. Keeping main small makes it easier to add platform-specific
 	// packaging later without mixing window setup, storage, and scheduler logic.
-	gui.Run()
+	gui.Run(hasArgument(core.StartInTrayArgument))
+}
+
+func hasArgument(argument string) bool {
+	for _, current := range os.Args[1:] {
+		if current == argument {
+			return true
+		}
+	}
+	return false
 }
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index 188c609..6426c4a 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -69,4 +69,5 @@ flowchart LR
 7. Autostart:
    The Settings tab calls the platform autostart implementation. Windows uses a
    shortcut in the current user's Startup folder. Linux uses a desktop-session
-   startup entry.
+   startup entry. Both autostart mechanisms pass `--start-in-tray`, so the
+   scheduler starts without opening the main window after sign-in.
diff --git a/src/core/autostart_linux.go b/src/core/autostart_linux.go
index 36a312c..f7e18cc 100644
--- a/src/core/autostart_linux.go
+++ b/src/core/autostart_linux.go
@@ -30,11 +30,11 @@ func SetAutostart(enabled bool, executablePath string, iconPath string) error {
 Type=Application
 Name=PySentry
 Comment=PySentry desktop scheduler
-Exec=%s
+Exec=%s %s
 %s
 Terminal=false
 X-GNOME-Autostart-enabled=true
-`, quoteDesktopExec(executablePath), desktopIconLine(iconPath))
+`, quoteDesktopExec(executablePath), StartInTrayArgument, desktopIconLine(iconPath))
 		return os.WriteFile(desktopPath, []byte(desktopFile), 0o644)
 	}
 
@@ -63,7 +63,8 @@ func AutostartStatus(expectedEnabled bool, executablePath string) (bool, string)
 	if readErr != nil {
 		return false, "Autostart desktop entry is missing"
 	}
-	if !strings.Contains(string(data), "Exec="+quoteDesktopExec(executablePath)) {
+	expectedExec := "Exec=" + quoteDesktopExec(executablePath) + " " + StartInTrayArgument
+	if !strings.Contains(string(data), expectedExec) {
 		return false, "Autostart desktop entry points to another executable"
 	}
 	return true, "Autostart is configured"
diff --git a/src/core/autostart_linux_test.go b/src/core/autostart_linux_test.go
new file mode 100644
index 0000000..facba5d
--- /dev/null
+++ b/src/core/autostart_linux_test.go
@@ -0,0 +1,32 @@
+//go:build linux
+
+package core
+
+import (
+	"os"
+	"strings"
+	"testing"
+)
+
+func TestLinuxAutostartStartsInTray(t *testing.T) {
+	t.Setenv("XDG_CONFIG_HOME", t.TempDir())
+
+	executablePath := "/opt/Go Sentry/gosentry"
+	if err := SetAutostart(true, executablePath, "/opt/Go Sentry/gosentry.png"); err != nil {
+		t.Fatalf("enable autostart: %v", err)
+	}
+
+	desktopPath, err := autostartDesktopPath()
+	if err != nil {
+		t.Fatalf("resolve desktop path: %v", err)
+	}
+	data, err := os.ReadFile(desktopPath)
+	if err != nil {
+		t.Fatalf("read desktop entry: %v", err)
+	}
+
+	expectedExec := "Exec=" + quoteDesktopExec(executablePath) + " " + StartInTrayArgument
+	if !strings.Contains(string(data), expectedExec) {
+		t.Fatalf("desktop entry does not start in tray: %s", data)
+	}
+}
diff --git a/src/core/autostart_windows.go b/src/core/autostart_windows.go
index f8be653..7e0b25e 100644
--- a/src/core/autostart_windows.go
+++ b/src/core/autostart_windows.go
@@ -57,13 +57,16 @@ func AutostartStatus(expectedEnabled bool, executablePath string) (bool, string)
 		return false, "Autostart shortcut cannot be checked"
 	}
 
-	actual, err := readShortcutTarget(shortcutPath)
+	actual, arguments, err := readShortcut(shortcutPath)
 	if err != nil {
 		return false, "Autostart shortcut cannot be read"
 	}
 	if !sameWindowsPath(actual, executablePath) {
 		return false, "Autostart shortcut points to another executable"
 	}
+	if strings.TrimSpace(arguments) != StartInTrayArgument {
+		return false, "Autostart shortcut does not start in tray"
+	}
 	return true, "Autostart is configured"
 }
 
@@ -84,11 +87,12 @@ func createStartupShortcut(shortcutPath string, executablePath string, iconPath
 	if iconPath == "" {
 		iconPath = executablePath
 	}
-	script := `$shell = New-Object -ComObject WScript.Shell; $shortcut = $shell.CreateShortcut($env:GOSENTRY_SHORTCUT_PATH); $shortcut.TargetPath = $env:GOSENTRY_TARGET_PATH; $shortcut.WorkingDirectory = $env:GOSENTRY_WORKING_DIRECTORY; $shortcut.IconLocation = $env:GOSENTRY_ICON_PATH; $shortcut.Save()`
+	script := `$shell = New-Object -ComObject WScript.Shell; $shortcut = $shell.CreateShortcut($env:GOSENTRY_SHORTCUT_PATH); $shortcut.TargetPath = $env:GOSENTRY_TARGET_PATH; $shortcut.Arguments = $env:GOSENTRY_ARGUMENTS; $shortcut.WorkingDirectory = $env:GOSENTRY_WORKING_DIRECTORY; $shortcut.IconLocation = $env:GOSENTRY_ICON_PATH; $shortcut.Save()`
 	command := exec.Command("powershell.exe", "-NoProfile", "-NonInteractive", "-ExecutionPolicy", "Bypass", "-Command", script)
 	command.Env = append(os.Environ(),
 		"GOSENTRY_SHORTCUT_PATH="+shortcutPath,
 		"GOSENTRY_TARGET_PATH="+executablePath,
+		"GOSENTRY_ARGUMENTS="+StartInTrayArgument,
 		"GOSENTRY_WORKING_DIRECTORY="+workingDirectory,
 		"GOSENTRY_ICON_PATH="+iconPath,
 	)
@@ -99,16 +103,27 @@ func createStartupShortcut(shortcutPath string, executablePath string, iconPath
 	return nil
 }
 
-func readShortcutTarget(shortcutPath string) (string, error) {
-	script := `$shell = New-Object -ComObject WScript.Shell; $shortcut = $shell.CreateShortcut($env:GOSENTRY_SHORTCUT_PATH); [Console]::Out.Write($shortcut.TargetPath)`
+func readShortcut(shortcutPath string) (string, string, error) {
+	script := `$shell = New-Object -ComObject WScript.Shell; $shortcut = $shell.CreateShortcut($env:GOSENTRY_SHORTCUT_PATH); [Console]::Out.Write($shortcut.TargetPath + [Environment]::NewLine + $shortcut.Arguments)`
 	command := exec.Command("powershell.exe", "-NoProfile", "-NonInteractive", "-ExecutionPolicy", "Bypass", "-Command", script)
 	command.Env = append(os.Environ(), "GOSENTRY_SHORTCUT_PATH="+shortcutPath)
 	configureHiddenWindow(command)
 	output, err := command.CombinedOutput()
 	if err != nil {
-		return "", fmt.Errorf("read startup shortcut: %w: %s", err, strings.TrimSpace(string(output)))
+		return "", "", fmt.Errorf("read startup shortcut: %w: %s", err, strings.TrimSpace(string(output)))
 	}
-	return strings.TrimSpace(string(output)), nil
+	lines := strings.SplitN(string(output), "\n", 2)
+	target := strings.TrimSpace(lines[0])
+	arguments := ""
+	if len(lines) > 1 {
+		arguments = strings.TrimSpace(lines[1])
+	}
+	return target, arguments, nil
+}
+
+func readShortcutTarget(shortcutPath string) (string, error) {
+	target, _, err := readShortcut(shortcutPath)
+	return target, err
 }
 
 func removeIfExists(path string) error {
diff --git a/src/core/autostart_windows_test.go b/src/core/autostart_windows_test.go
index a6355d2..f085eb0 100644
--- a/src/core/autostart_windows_test.go
+++ b/src/core/autostart_windows_test.go
@@ -63,11 +63,14 @@ func TestCreateStartupShortcutHandlesSpaces(t *testing.T) {
 		t.Fatalf("create shortcut: %v", err)
 	}
 
-	actual, err := readShortcutTarget(shortcutPath)
+	actual, arguments, err := readShortcut(shortcutPath)
 	if err != nil {
 		t.Fatalf("read shortcut: %v", err)
 	}
 	if !sameWindowsPath(actual, targetPath) {
 		t.Fatalf("shortcut target mismatch: got %q want %q", actual, targetPath)
 	}
+	if arguments != StartInTrayArgument {
+		t.Fatalf("shortcut arguments mismatch: got %q want %q", arguments, StartInTrayArgument)
+	}
 }
diff --git a/src/core/model.go b/src/core/model.go
index c92ec34..dd55e96 100644
--- a/src/core/model.go
+++ b/src/core/model.go
@@ -2,6 +2,11 @@ package core
 
 import "time"
 
+// StartInTrayArgument is written to the Windows Startup shortcut so autostart
+// can keep the scheduler running without flashing the main window. Manual
+// launches omit this flag and open the normal window.
+const StartInTrayArgument = "--start-in-tray"
+
 // Config is stored in pysentry.yaml next to the program. It contains only
 // application-level choices: where to read jobs from, where to write logs, and
 // how the desktop shell should behave.
diff --git a/src/gui/app.go b/src/gui/app.go
index 288632e..2e74cfd 100644
--- a/src/gui/app.go
+++ b/src/gui/app.go
@@ -42,9 +42,9 @@ const singleInstanceShowCommand = "show"
 type job = core.Job
 type event = core.RunRecord
 
-func Run() {
+func Run(startInTray bool) {
 	started := time.Now()
-	instanceListener, primary := acquireSingleInstance()
+	instanceListener, primary := acquireSingleInstance(!startInTray)
 	if !primary {
 		return
 	}
@@ -62,6 +62,10 @@ func Run() {
 	w.Resize(fyne.NewSize(1120, 720))
 	w.SetContent(newMainView(w, started))
 	serveSingleInstance(instanceListener, w)
+	if startInTray {
+		a.Run()
+		return
+	}
 	w.ShowAndRun()
 }
 
@@ -96,7 +100,7 @@ func configureSystemTray(a fyne.App, w fyne.Window) {
 	})
 }
 
-func acquireSingleInstance() (net.Listener, bool) {
+func acquireSingleInstance(showExisting bool) (net.Listener, bool) {
 	listener, err := net.Listen("tcp", singleInstanceAddress)
 	if err == nil {
 		return listener, true
@@ -104,7 +108,9 @@ func acquireSingleInstance() (net.Listener, bool) {
 
 	connection, dialErr := net.DialTimeout("tcp", singleInstanceAddress, time.Second)
 	if dialErr == nil {
-		_, _ = io.WriteString(connection, singleInstanceShowCommand)
+		if showExisting {
+			_, _ = io.WriteString(connection, singleInstanceShowCommand)
+		}
 		_ = connection.Close()
 		return nil, false
 	}