diff --git a/flake.lock b/flake.lock
index 07c8f8b86..b01674bec 100644
--- a/flake.lock
+++ b/flake.lock
@@ -18,6 +18,24 @@
         "type": "github"
       }
     },
+    "flake-utils_2": {
+      "inputs": {
+        "systems": "systems_2"
+      },
+      "locked": {
+        "lastModified": 1701680307,
+        "narHash": "sha256-kAuep2h5ajznlPMD9rnQyffWG8EM/C73lejGofXvdM8=",
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "rev": "4022d587cbbfd70fe950c1e2083a02621806a725",
+        "type": "github"
+      },
+      "original": {
+        "owner": "numtide",
+        "repo": "flake-utils",
+        "type": "github"
+      }
+    },
     "nixpkgs": {
       "locked": {
         "lastModified": 1748437600,
@@ -34,10 +52,32 @@
         "type": "github"
       }
     },
+    "pnpm2nix": {
+      "inputs": {
+        "flake-utils": "flake-utils_2",
+        "nixpkgs": [
+          "nixpkgs"
+        ]
+      },
+      "locked": {
+        "lastModified": 1748881470,
+        "narHash": "sha256-Uk4J9StEEH/JaJQ+cw7wVvgLPMLZNoOGDGxKSbSDXyc=",
+        "owner": "FliegendeWurst",
+        "repo": "pnpm2nix-nzbr",
+        "rev": "85497400540854c2895b9f59b5cc741a1f838da2",
+        "type": "github"
+      },
+      "original": {
+        "owner": "FliegendeWurst",
+        "repo": "pnpm2nix-nzbr",
+        "type": "github"
+      }
+    },
     "root": {
       "inputs": {
         "flake-utils": "flake-utils",
-        "nixpkgs": "nixpkgs"
+        "nixpkgs": "nixpkgs",
+        "pnpm2nix": "pnpm2nix"
       }
     },
     "systems": {
@@ -54,6 +94,21 @@
         "repo": "default",
         "type": "github"
       }
+    },
+    "systems_2": {
+      "locked": {
+        "lastModified": 1681028828,
+        "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+        "owner": "nix-systems",
+        "repo": "default",
+        "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nix-systems",
+        "repo": "default",
+        "type": "github"
+      }
     }
   },
   "root": "root",
diff --git a/flake.nix b/flake.nix
index 4ffa16168..19a366992 100644
--- a/flake.nix
+++ b/flake.nix
@@ -4,6 +4,10 @@
   inputs = {
     nixpkgs.url = "github:nixos/nixpkgs/nixos-25.05";
     flake-utils.url = "github:numtide/flake-utils";
+    pnpm2nix = {
+      url = "github:FliegendeWurst/pnpm2nix-nzbr";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
   };
 
   outputs =
@@ -11,69 +15,164 @@
       self,
       nixpkgs,
       flake-utils,
+      pnpm2nix,
     }:
     flake-utils.lib.eachDefaultSystem (
       system:
       let
-        packageJSON = builtins.fromJSON (builtins.readFile ./package.json);
         pkgs = import nixpkgs { inherit system; };
         electron = pkgs.electron_35;
+        nodejs = pkgs.nodejs_22;
+        pnpm = pkgs.pnpm_10;
         inherit (pkgs)
           copyDesktopItems
+          darwin
           lib
           makeBinaryWrapper
           makeDesktopItem
-          nodejs
-          pnpm
+          removeReferencesTo
           stdenv
           wrapGAppsHook3
           xcodebuild
-          darwin
           ;
-        desktop = stdenv.mkDerivation (finalAttrs: {
-          pname = "triliumnext-desktop";
-          version = packageJSON.version;
-          src = lib.cleanSource ./.;
 
-          nativeBuildInputs =
-            [
-              pnpm.configHook
-              nodejs
-              nodejs.python
-              copyDesktopItems
-              makeBinaryWrapper
-              wrapGAppsHook3
-            ]
-            ++ lib.optionals stdenv.hostPlatform.isDarwin [
-              xcodebuild
-              darwin.cctools
+        fullCleanSourceFilter =
+          name: type:
+          (lib.cleanSourceFilter name type)
+          || (
+            let
+              baseName = baseNameOf (toString name);
+            in
+            # No need to copy the flake.
+            # Don't copy local development instance of NX cache.
+            baseName == "flake.nix" || baseName == "flake.lock" || baseName == ".nx"
+          );
+        fullCleanSource =
+          src:
+          lib.cleanSourceWith {
+            filter = fullCleanSourceFilter;
+            src = src;
+          };
+        packageJson = builtins.fromJSON (builtins.readFile ./package.json);
+
+        makeApp =
+          {
+            app,
+            buildTask,
+            mainProgram,
+            installCommands,
+            preBuildCommands ? "",
+          }:
+          pnpm2nix.packages.${system}.mkPnpmPackage rec {
+            pname = "triliumnext-${app}";
+            version = packageJson.version + (lib.optionalString (self ? shortRev) "-${self.shortRev}");
+
+            src = fullCleanSource ./.;
+            packageJSON = ./package.json;
+            pnpmLockYaml = ./pnpm-lock.yaml;
+
+            workspace = fullCleanSource ./.;
+            pnpmWorkspaceYaml = ./pnpm-workspace.yaml;
+
+            inherit nodejs pnpm;
+
+            extraNodeModuleSources = [
+              rec {
+                name = "patches";
+                value = ./patches;
+              }
             ];
 
-          dontWrapGApps = true;
+            postConfigure =
+              ''
+                chmod +x node_modules/.pnpm/electron@*/node_modules/electron/install.js
+                patchShebangs --build node_modules
+              ''
+              + lib.optionalString stdenv.hostPlatform.isLinux ''
+                patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
+                  node_modules/.pnpm/sass-embedded-linux-x64@*/node_modules/sass-embedded-linux-x64/dart-sass/src/dart
+              '';
 
-          preBuild = lib.optionalString stdenv.hostPlatform.isLinux ''
-            patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
-              node_modules/.pnpm/sass-embedded-linux-x64@*/node_modules/sass-embedded-linux-x64/dart-sass/src/dart
-          '';
+            extraNativeBuildInputs =
+              [
+                makeBinaryWrapper
+                nodejs.python
+                removeReferencesTo
+              ]
+              ++ lib.optionals (app == "desktop") [
+                copyDesktopItems
+                wrapGAppsHook3
+              ]
+              ++ lib.optionals stdenv.hostPlatform.isDarwin [
+                xcodebuild
+                darwin.cctools
+              ];
+            dontWrapGApps = true;
 
-          buildPhase = ''
-            runHook preBuild
+            env.ELECTRON_SKIP_BINARY_DOWNLOAD = "1";
 
-            # Disable NX interaction
-            export NX_TUI=false
-            export NX_DAEMON=false
+            preBuild = ''
+              ${preBuildCommands}
+            '';
 
-            pnpm nx run desktop:build --outputStyle stream --verbose
+            scriptFull = "pnpm nx ${buildTask} --outputStyle stream --verbose";
 
-            # Rebuild dependencies
-            export npm_config_nodedir=${electron.headers}
-            pnpm nx run desktop:rebuild-deps --outputStyle stream --verbose
+            installPhase = ''
+              runHook preInstall
 
-            runHook postBuild
-          '';
+              ${installCommands}
 
-          installPhase = ''
-            runHook preInstall
+              runHook postInstall
+            '';
+
+            components = [
+              "packages/ckeditor5"
+              "packages/ckeditor5-admonition"
+              "packages/ckeditor5-footnotes"
+              "packages/ckeditor5-keyboard-marker"
+              "packages/ckeditor5-math"
+              "packages/ckeditor5-mermaid"
+              "packages/codemirror"
+              "packages/commons"
+              "packages/express-partial-content"
+              "packages/highlightjs"
+              "packages/turndown-plugin-gfm"
+
+              "apps/client"
+              "apps/db-compare"
+              "apps/desktop"
+              "apps/dump-db"
+              "apps/edit-docs"
+              "apps/server"
+              "apps/server-e2e"
+            ];
+
+            desktopItems = lib.optionals (app == "desktop") [
+              (makeDesktopItem {
+                name = "TriliumNext Notes";
+                exec = meta.mainProgram;
+                icon = "trilium";
+                comment = meta.description;
+                desktopName = "TriliumNext Notes";
+                categories = [ "Office" ];
+                startupWMClass = "Trilium Notes Next";
+              })
+            ];
+
+            meta = {
+              description = "TriliumNext: ${app}";
+              inherit mainProgram;
+            };
+          };
+
+        desktop = makeApp {
+          app = "desktop";
+          preBuildCommands = "export npm_config_nodedir=${electron.headers}";
+          buildTask = "run desktop:rebuild-deps";
+          mainProgram = "trilium";
+          installCommands = ''
+            remove-references-to -t ${electron.headers} apps/desktop/dist/node_modules/better-sqlite3/build/config.gypi
+            remove-references-to -t ${nodejs.python} apps/desktop/dist/node_modules/better-sqlite3/build/config.gypi
 
             mkdir -p $out/{bin,share/icons/hicolor/512x512/apps,opt/trilium}
             cp --archive apps/desktop/dist/* $out/opt/trilium
@@ -82,34 +181,29 @@
               "''${gappsWrapperArgs[@]}" \
               --set-default ELECTRON_IS_DEV 0 \
               --add-flags $out/opt/trilium/main.cjs
-
-            runHook postInstall
           '';
+        };
 
-          desktopItems = [
-            (makeDesktopItem {
-              name = "TriliumNext Notes";
-              exec = finalAttrs.meta.mainProgram;
-              icon = "trilium";
-              comment = finalAttrs.meta.description;
-              desktopName = "TriliumNext Notes";
-              categories = [ "Office" ];
-              startupWMClass = "Trilium Notes Next";
-            })
-          ];
+        server = makeApp {
+          app = "server";
+          preBuildCommands = "pushd apps/server; pnpm rebuild; popd";
+          buildTask = "--project=server build";
+          mainProgram = "trilium-server";
+          installCommands = ''
+            remove-references-to -t ${nodejs.python} apps/server/dist/node_modules/better-sqlite3/build/config.gypi
+            remove-references-to -t ${pnpm} apps/server/dist/node_modules/better-sqlite3/build/config.gypi
 
-          pnpmDeps = pnpm.fetchDeps {
-            inherit (finalAttrs) pname version src;
-            hash = "sha256-xC0u1h92wtthylOAw+IF9mpFi0c4xajJhUcA9pqzcAw=";
-          };
-
-          meta = {
-            description = "Free and open-source, cross-platform hierarchical note taking application with focus on building large personal knowledge bases";
-            mainProgram = "trilium";
-          };
-        });
+            mkdir -p $out/{bin,opt/trilium-server}
+            cp --archive apps/server/dist/* $out/opt/trilium-server
+            makeWrapper ${lib.getExe nodejs} $out/bin/trilium-server \
+              --add-flags $out/opt/trilium-server/main.cjs
+          '';
+        };
       in
       {
+        packages.desktop = desktop;
+        packages.server = server;
+
         packages.default = desktop;
       }
     );