diff --git a/examples/development/php/php8.1/devbox.json b/examples/development/php/php8.1/devbox.json
index 4b6f2849940..c3243a776a8 100644
--- a/examples/development/php/php8.1/devbox.json
+++ b/examples/development/php/php8.1/devbox.json
@@ -1,6 +1,5 @@
 {
   "packages": [
-    "php81Packages.composer@latest",
     "php81Extensions.xdebug@latest",
     "php81Extensions.imagick@latest",
     "php@8.1"
diff --git a/examples/development/php/php8.1/devbox.lock b/examples/development/php/php8.1/devbox.lock
index 66389caea3e..fba3ff2b709 100644
--- a/examples/development/php/php8.1/devbox.lock
+++ b/examples/development/php/php8.1/devbox.lock
@@ -40,26 +40,6 @@
         }
       }
     },
-    "php81Packages.composer@latest": {
-      "last_modified": "2023-08-30T00:25:28Z",
-      "resolved": "github:NixOS/nixpkgs/a63a64b593dcf2fe05f7c5d666eb395950f36bc9#php81Packages.composer",
-      "source": "devbox-search",
-      "version": "2.5.8",
-      "systems": {
-        "aarch64-darwin": {
-          "store_path": "/nix/store/7hxmkxa9bmaplyy1ixl0yxv3j0qvxvc3-php-composer-2.5.8"
-        },
-        "aarch64-linux": {
-          "store_path": "/nix/store/vwrbpz9wr7blr7alx0fl3x79ym3jbdqa-php-composer-2.5.8"
-        },
-        "x86_64-darwin": {
-          "store_path": "/nix/store/fjy357jpj9q2bfahsgnak4mrh8y07izw-php-composer-2.5.8"
-        },
-        "x86_64-linux": {
-          "store_path": "/nix/store/6w2vrfjdwhr3mj1magr2rmbycln379f8-php-composer-2.5.8"
-        }
-      }
-    },
     "php@8.1": {
       "last_modified": "2023-09-04T16:24:30Z",
       "plugin_version": "0.0.2",
diff --git a/internal/impl/devbox.go b/internal/impl/devbox.go
index e45dbb4163f..47327ab1551 100644
--- a/internal/impl/devbox.go
+++ b/internal/impl/devbox.go
@@ -963,14 +963,7 @@ func (d *Devbox) InstallablePackages() []*devpkg.Package {
 // packages concatenated in correct order
 func (d *Devbox) AllInstallablePackages() ([]*devpkg.Package, error) {
 	userPackages := d.InstallablePackages()
-	pluginPackages, err := d.PluginManager().PluginPackages(userPackages)
-	if err != nil {
-		return nil, err
-	}
-	// We prioritize plugin packages so that the php plugin works. Not sure
-	// if this is behavior we want for user plugins. We may need to add an optional
-	// priority field to the config.
-	return append(pluginPackages, userPackages...), nil
+	return d.PluginManager().ProcessPluginPackages(userPackages)
 }
 
 func (d *Devbox) Includes() []plugin.Includable {
diff --git a/internal/plugin/manager.go b/internal/plugin/manager.go
index bbc14ad3ffa..282d58a3db7 100644
--- a/internal/plugin/manager.go
+++ b/internal/plugin/manager.go
@@ -4,6 +4,7 @@
 package plugin
 
 import (
+	"github.com/samber/lo"
 	"go.jetpack.io/devbox/internal/devpkg"
 	"go.jetpack.io/devbox/internal/lock"
 )
@@ -45,16 +46,31 @@ func (m *Manager) ApplyOptions(opts ...managerOption) {
 	}
 }
 
-func (m *Manager) PluginPackages(inputs []*devpkg.Package) ([]*devpkg.Package, error) {
-	result := []*devpkg.Package{}
-	for _, input := range inputs {
-		config, err := getConfigIfAny(input, m.ProjectDir())
+// ProcessPluginPackages adds and removes packages as indicated by plugins
+func (m *Manager) ProcessPluginPackages(
+	userPackages []*devpkg.Package,
+) ([]*devpkg.Package, error) {
+	pluginPackages := []*devpkg.Package{}
+	packagesToRemove := []*devpkg.Package{}
+	for _, pkg := range userPackages {
+		config, err := getConfigIfAny(pkg, m.ProjectDir())
 		if err != nil {
 			return nil, err
 		} else if config == nil {
 			continue
 		}
-		result = append(result, devpkg.PackageFromStrings(config.Packages, m.lockfile)...)
+		pluginPackages = append(
+			pluginPackages,
+			devpkg.PackageFromStrings(config.Packages, m.lockfile)...,
+		)
+		if config.RemoveTriggerPackage {
+			packagesToRemove = append(packagesToRemove, pkg)
+		}
 	}
-	return result, nil
+
+	netUserPackages, _ := lo.Difference(userPackages, packagesToRemove)
+	// We prioritize plugin packages so that the php plugin works. Not sure
+	// if this is behavior we want for user plugins. We may need to add an optional
+	// priority field to the config.
+	return append(pluginPackages, netUserPackages...), nil
 }
diff --git a/internal/plugin/plugin.go b/internal/plugin/plugin.go
index 9552bdebfd8..68b0503a005 100644
--- a/internal/plugin/plugin.go
+++ b/internal/plugin/plugin.go
@@ -43,6 +43,9 @@ type config struct {
 	Packages    []string          `json:"__packages"`
 	Env         map[string]string `json:"env"`
 	Readme      string            `json:"readme"`
+	// If true, we remove the package that triggered this plugin from the environment
+	// Useful when we want to replace with flake
+	RemoveTriggerPackage bool `json:"__remove_trigger_package,omitempty"`
 
 	Shell struct {
 		// InitHook contains commands that will run at shell startup.
diff --git a/plugins/haskell.json b/plugins/haskell.json
index e87d25b4b40..33122393797 100644
--- a/plugins/haskell.json
+++ b/plugins/haskell.json
@@ -5,6 +5,7 @@
   "__packages": [
     "path:{{ .Virtenv }}"
   ],
+  "__remove_trigger_package": true,
   "create_files": {
     "{{ .Virtenv }}/flake.nix": "haskell/flake.nix"
   }
diff --git a/plugins/mariadb.json b/plugins/mariadb.json
index d32b8c95551..3750b7a50ac 100644
--- a/plugins/mariadb.json
+++ b/plugins/mariadb.json
@@ -18,6 +18,7 @@
   "__packages": [
     "path:{{ .Virtenv }}"
   ],
+  "__remove_trigger_package": true,
   "shell": {
     "init_hook": [
       "bash {{ .Virtenv }}/setup_db.sh"
diff --git a/plugins/mysql.json b/plugins/mysql.json
index 6ce809f184e..75bd335751b 100644
--- a/plugins/mysql.json
+++ b/plugins/mysql.json
@@ -18,6 +18,7 @@
     "__packages": [
       "path:{{ .Virtenv }}"
     ],
+    "__remove_trigger_package": true,
     "shell": {
       "init_hook": [
         "bash {{ .Virtenv }}/setup_db.sh"
diff --git a/plugins/php.json b/plugins/php.json
index feb839c0c2f..620c3168352 100644
--- a/plugins/php.json
+++ b/plugins/php.json
@@ -6,6 +6,7 @@
     "path:{{ .Virtenv }}",
     "path:{{ .Virtenv }}#composer"
   ],
+  "__remove_trigger_package": true,
   "env": {
     "PHPFPM_ERROR_LOG_FILE": "{{ .Virtenv }}/php-fpm.log",
     "PHPFPM_PID_FILE": "{{ .Virtenv }}/php-fpm.pid",