diff --git a/cmd/fml/fml.go b/cmd/fml/fml.go
index f15b522..9769bc5 100644
--- a/cmd/fml/fml.go
+++ b/cmd/fml/fml.go
@@ -14,9 +14,10 @@ import (
 )
 
 type config struct {
-	modsdir, infile, outfile          string
-	mods                              modlist.Modlist
-	clobber, addmissing, missingstate bool
+	modsdir, infile, outfile        string
+	mods                            modlist.Modlist
+	clobber, addmissing             bool
+	missingstate, ignoreuninstalled bool
 }
 
 var cfg config
@@ -85,6 +86,12 @@ func main() {
 				Required: false,
 				Usage:    "Missing mods are added in enabled state",
 			},
+			&cli.BoolFlag{
+				Name:     "ignore-uninstalled",
+				Aliases:  []string{"u"},
+				Required: false,
+				Usage:    "Missing mod archives are ignored",
+			},
 		},
 		Before: func(ctx *cli.Context) error {
 			// Setup logger
@@ -100,6 +107,7 @@ func main() {
 			cfg.clobber = ctx.Bool("clobber")
 			cfg.addmissing = !ctx.Bool("no-add-missing")
 			cfg.missingstate = ctx.Bool("enable-missing")
+			cfg.ignoreuninstalled = ctx.Bool("ignore-uninstalled")
 
 			// Deal with in/out file
 			var in = ctx.String("infile")
@@ -125,13 +133,20 @@ func main() {
 		Action: func(ctx *cli.Context) error {
 			var err error
 
-			cfg.mods, err = modlist.ReadFromFile(cfg.infile)
+			cfg.mods, err = modlist.ReadFromFile(cfg.infile, cfg.modsdir)
 			if err != nil {
 				return err
 			}
 
 			if cfg.addmissing {
-				err = modlist.AddModsNotInList(cfg.modsdir, &cfg.mods, cfg.missingstate)
+				err = cfg.mods.AddModsNotInList(cfg.missingstate)
+				if err != nil {
+					return err
+				}
+			}
+
+			if !cfg.ignoreuninstalled {
+				err = cfg.mods.RemoveModsNotInFolder()
 				if err != nil {
 					return err
 				}
diff --git a/internal/modlist/modlist.go b/internal/modlist/modlist.go
index 22e55df..2d7a2ba 100644
--- a/internal/modlist/modlist.go
+++ b/internal/modlist/modlist.go
@@ -22,6 +22,7 @@ type Mod struct {
 
 // Modlist holds a slice of mods.
 type Modlist struct {
+	dir  string
 	Mods []Mod `json:"mods"`
 }
 
@@ -119,8 +120,73 @@ func (modlist *Modlist) String() {
 	modlist.Print("mods")
 }
 
+// AddModsNotInList finds mod archives in the mod folder that aren't in the modlist, and adds them.
+func (modlist *Modlist) AddModsNotInList(state bool) error {
+	r := regexp.MustCompile(fileRegex)
+
+	files, err := os.ReadDir(modlist.dir)
+	if err != nil {
+		return err
+	}
+
+	for _, file := range files {
+		if strings.HasSuffix(file.Name(), ".zip") && !file.IsDir() {
+			groups := r.FindAllStringSubmatch(file.Name(), -1)
+			name := groups[0][1]
+			version := groups[0][2]
+
+			if !modlist.HasMod(name) {
+				log.Infof("Found %s not in modlist, adding v%s in disabled state.", name, version)
+				modlist.Mods = append(modlist.Mods, Mod{
+					Name:    name,
+					Enabled: state,
+				})
+			}
+		}
+	}
+
+	return nil
+}
+
+// RemoveModsNotInFolder removes mods from the modlist if a corresponding
+// zip file cannot be found in the mods dir.
+func (modlist *Modlist) RemoveModsNotInFolder() error {
+	for i, mod := range modlist.Mods {
+		in, err := isModInFolder(mod.Name, modlist.dir)
+		if !in && err == nil {
+			log.Warnf("Zip file for %s could not be found, removing!", mod.Name)
+			// mods.Mods[i] = nil
+			modlist.Mods = append(modlist.Mods[:i], modlist.Mods[i+1:]...)
+		} else if err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
 /// Functions related to the modlist but that shouldn't be attached to the types
 
+func isModInFolder(modname, modsdir string) (bool, error) {
+	if modname == "base" {
+		return true, nil
+	}
+
+	// TODO: try for less O(n)
+	files, err := os.ReadDir(modsdir)
+	if err != nil {
+		return false, err
+	}
+
+	for _, file := range files {
+		if strings.HasPrefix(file.Name(), modname) {
+			return true, nil
+		}
+	}
+
+	return false, nil
+}
+
 // WriteToFile writes the modlist to the given filename.
 func WriteToFile(filename string, mods *Modlist) error {
 	data, err := json.MarshalIndent(&mods, "", "  ")
@@ -134,8 +200,10 @@ func WriteToFile(filename string, mods *Modlist) error {
 }
 
 // ReadFromFile reads the modlist from the given filename.
-func ReadFromFile(filename string) (Modlist, error) {
-	var mods Modlist = Modlist{}
+func ReadFromFile(filename, modsdir string) (Modlist, error) {
+	var mods Modlist = Modlist{
+		dir: modsdir,
+	}
 
 	data, err := os.ReadFile(filename)
 	if err != nil {
@@ -150,31 +218,3 @@ func ReadFromFile(filename string) (Modlist, error) {
 	log.Infof("Read modlist from file %s.", filename)
 	return mods, nil
 }
-
-// AddModsNotInList finds mod archives in the mod folder that aren't in the modlist, and adds them.
-func AddModsNotInList(modsdir string, mods *Modlist, state bool) error {
-	r := regexp.MustCompile(fileRegex)
-
-	files, err := os.ReadDir(modsdir)
-	if err != nil {
-		return err
-	}
-
-	for _, file := range files {
-		if strings.HasSuffix(file.Name(), ".zip") && !file.IsDir() {
-			groups := r.FindAllStringSubmatch(file.Name(), -1)
-			name := groups[0][1]
-			version := groups[0][2]
-
-			if !mods.HasMod(name) {
-				log.Infof("Found %s not in modlist, adding v%s in disabled state.", name, version)
-				mods.Mods = append(mods.Mods, Mod{
-					Name:    name,
-					Enabled: state,
-				})
-			}
-		}
-	}
-
-	return nil
-}