diff --git a/src/scaffold/app/nix.rs b/src/scaffold/app/nix.rs
index 55864e390..57fda1978 100644
--- a/src/scaffold/app/nix.rs
+++ b/src/scaffold/app/nix.rs
@@ -7,10 +7,11 @@ use std::process::{Command, Stdio};
 
 use crate::error::{ScaffoldError, ScaffoldResult};
 use crate::file_tree::*;
+use crate::scaffold::web_app::package_manager::PackageManager;
 
 use super::git::is_inside_work_tree;
 
-pub fn flake_nix(holo_enabled: bool) -> FileTree {
+pub fn flake_nix(holo_enabled: bool, package_manager: &PackageManager) -> FileTree {
     let holo_inputs = holo_enabled
         .then_some(
             r#"
@@ -52,17 +53,17 @@ pub fn flake_nix(holo_enabled: bool) -> FileTree {
           rust # For Rust development, with the WASM target included for zome builds
         ]) ++ (with pkgs; [
           nodejs_20
-          nodePackages.pnpm
-          yarn-berry
-          bun
           binaryen
           {}
+          {}
         ]);
       }};
     }};
   }};
 }}"#,
-        holo_inputs, holo_packages
+        holo_inputs,
+        package_manager.nixpkg().unwrap_or_default(),
+        holo_packages
     ))
 }
 
diff --git a/src/scaffold/web_app.rs b/src/scaffold/web_app.rs
index f76a95d9d..9b948ac01 100644
--- a/src/scaffold/web_app.rs
+++ b/src/scaffold/web_app.rs
@@ -42,7 +42,10 @@ pub fn scaffold_web_app(
         app_file_tree
             .dir_content_mut()
             .ok_or(ScaffoldError::PathNotFound(PathBuf::new()))?
-            .insert("flake.nix".into(), flake_nix(holo_enabled));
+            .insert(
+                "flake.nix".into(),
+                flake_nix(holo_enabled, &package_manager),
+            );
     }
 
     if package_manager == PackageManager::Pnpm {
diff --git a/src/scaffold/web_app/package_manager.rs b/src/scaffold/web_app/package_manager.rs
index c5939f417..6755679fe 100644
--- a/src/scaffold/web_app/package_manager.rs
+++ b/src/scaffold/web_app/package_manager.rs
@@ -46,6 +46,18 @@ impl PackageManager {
         Ok(managers[selection])
     }
 
+    /// Get's the the package manager's nixpkg that should be used with the generated
+    /// flake.nix
+    pub fn nixpkg(&self) -> Option<&str> {
+        match self {
+            PackageManager::Bun => Some("bun"),
+            PackageManager::Pnpm => Some("nodePackages.pnpm"),
+            PackageManager::Yarn => Some("yarn-berry"),
+            // npm is already included with nodejs_20
+            PackageManager::Npm => None,
+        }
+    }
+
     /// Checks if the specified lockfile exists in the provided file tree.
     pub fn lockfile_exists(app_file_tree: &FileTree, path: &Path) -> bool {
         let v = path
diff --git a/templates/custom-template/custom-template/flake.nix b/templates/custom-template/custom-template/flake.nix
index fe9fcc2c3..9e90f5bc5 100644
--- a/templates/custom-template/custom-template/flake.nix
+++ b/templates/custom-template/custom-template/flake.nix
@@ -25,9 +25,6 @@
           rust # For Rust development, with the WASM target included for zome builds
         ]) ++ (with pkgs; [
           nodejs_20
-          nodePackages.pnpm
-          yarn
-          bun
           binaryen
         ]);
       };