diff --git a/cmd/incus/main.go b/cmd/incus/main.go
index ce0fda48d8c..bc435fe0672 100644
--- a/cmd/incus/main.go
+++ b/cmd/incus/main.go
@@ -92,14 +92,7 @@ func aliases() []string {
 	return aliases
 }
 
-func main() {
-	// Process aliases
-	err := execIfAliases()
-	if err != nil {
-		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
-		os.Exit(1)
-	}
-
+func createApp() (*cobra.Command, *cmdGlobal) {
 	// Setup the parser
 	app := &cobra.Command{}
 	app.Use = "incus"
@@ -306,8 +299,14 @@ Custom commands can be defined through aliases, use "incus alias" to control tho
 	app.Flags().BoolVar(&globalCmd.flagHelpAll, "all", false, i18n.G("Show less common commands"))
 	help.Flags().BoolVar(&globalCmd.flagHelpAll, "all", false, i18n.G("Show less common commands"))
 
-	// Deal with --all flag and --sub-commands flag
-	err = app.ParseFlags(os.Args[1:])
+	return app, &globalCmd
+}
+
+func main() {
+	app, globalCmd := createApp()
+
+	// Deal with --all and --sub-commands flags as well as process aliases.
+	err := app.ParseFlags(os.Args[1:])
 	if err == nil {
 		if globalCmd.flagHelpAll {
 			// Show all commands
@@ -325,6 +324,13 @@ Custom commands can be defined through aliases, use "incus alias" to control tho
 		}
 	}
 
+	// Process aliases
+	err = execIfAliases(app)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+		os.Exit(1)
+	}
+
 	// Run the main command and handle errors
 	err = app.Execute()
 	if err != nil {
diff --git a/cmd/incus/main_aliases.go b/cmd/incus/main_aliases.go
index 64f29acebfd..d02bb9179da 100644
--- a/cmd/incus/main_aliases.go
+++ b/cmd/incus/main_aliases.go
@@ -10,6 +10,7 @@ import (
 	"strings"
 
 	"github.com/kballard/go-shellquote"
+	"github.com/spf13/cobra"
 
 	"github.com/lxc/incus/v6/internal/i18n"
 	config "github.com/lxc/incus/v6/shared/cliconfig"
@@ -76,26 +77,36 @@ func findAlias(aliases map[string]string, origArgs []string) ([]string, []string
 	return aliasKey, aliasValue, foundAlias
 }
 
-func expandAlias(conf *config.Config, args []string) ([]string, bool, error) {
-	var completion = false
-	var completionFrament string
-	var newArgs []string
-	var origArgs []string
+func expandAlias(conf *config.Config, args []string, app *cobra.Command) ([]string, bool, error) {
+	fset := app.Flags()
 
-	for _, arg := range args[1:] {
-		if !strings.HasPrefix(arg, "-") {
-			break
-		}
+	nargs := fset.NArg()
+	firstArgIndex := 1
+	firstPosArgIndex := 0
+	if fset.Arg(0) == "__complete" {
+		nargs--
+		firstArgIndex++
+		firstPosArgIndex++
+	}
 
-		newArgs = append(newArgs, arg)
+	if nargs == 0 {
+		return nil, false, nil
 	}
 
-	origArgs = append([]string{args[0]}, args[len(newArgs)+1:]...)
+	lastFlagIndex := slices.Index(args, fset.Arg(firstPosArgIndex))
+
+	// newArgs contains all the flags before the first positional argument
+	newArgs := args[firstArgIndex:lastFlagIndex]
+
+	// origArgs contains everything except the flags in newArgs
+	origArgs := slices.Concat(args[:firstArgIndex], args[lastFlagIndex:])
 
 	// strip out completion subcommand and fragment from end
+	completion := false
+	completionFragment := ""
 	if len(origArgs) >= 3 && origArgs[1] == "__complete" {
 		completion = true
-		completionFrament = origArgs[len(origArgs)-1]
+		completionFragment = origArgs[len(origArgs)-1]
 		origArgs = append(origArgs[:1], origArgs[2:len(origArgs)-1]...)
 	}
 
@@ -189,7 +200,7 @@ func expandAlias(conf *config.Config, args []string) ([]string, bool, error) {
 	// add back in completion if it was stripped before
 	if completion {
 		newArgs = append([]string{newArgs[0], "__complete"}, newArgs[1:]...)
-		newArgs = append(newArgs, completionFrament)
+		newArgs = append(newArgs, completionFragment)
 	}
 
 	// Add the rest of the arguments only if @ARGS@ wasn't used.
@@ -200,9 +211,7 @@ func expandAlias(conf *config.Config, args []string) ([]string, bool, error) {
 	return newArgs, true, nil
 }
 
-func execIfAliases() error {
-	args := os.Args
-
+func execIfAliases(app *cobra.Command) error {
 	// Avoid loops
 	if os.Getenv("INCUS_ALIASES") == "1" {
 		return nil
@@ -214,7 +223,7 @@ func execIfAliases() error {
 	}
 
 	// Expand the aliases
-	newArgs, expanded, err := expandAlias(conf, args)
+	newArgs, expanded, err := expandAlias(conf, os.Args, app)
 	if err != nil {
 		return err
 	} else if !expanded {
diff --git a/cmd/incus/main_test.go b/cmd/incus/main_test.go
index ff6eb2ca2ca..29bfc24b18a 100644
--- a/cmd/incus/main_test.go
+++ b/cmd/incus/main_test.go
@@ -84,12 +84,22 @@ func TestExpandAliases(t *testing.T) {
 			input:    []string{"incus", "snapshots", "with", "recursion", "c1", "2"},
 			expected: []string{"incus", "query", "/1.0/instances/c1/snapshots?recursion=2"},
 		},
+		{
+			input:    []string{"incus", "--project", "default", "fizz", "c1", "buzz"},
+			expected: []string{"incus", "--project", "default", "exec", "c1", "--", "echo", "buzz"},
+		},
+		{
+			input:    []string{"incus", "--project=default", "fizz", "c1", "buzz"},
+			expected: []string{"incus", "--project=default", "exec", "c1", "--", "echo", "buzz"},
+		},
 	}
 
 	conf := &config.Config{Aliases: aliases}
 
 	for _, tc := range testcases {
-		result, expanded, err := expandAlias(conf, tc.input)
+		app, _ := createApp()
+		_ = app.ParseFlags(tc.input[1:])
+		result, expanded, err := expandAlias(conf, tc.input, app)
 		if tc.expectErr {
 			assert.Error(t, err)
 			continue