diff --git a/pkgs/development/python-modules/phonopy/default.nix b/pkgs/development/python-modules/phonopy/default.nix
index b178b881c0c1..1f3fd633936f 100644
--- a/pkgs/development/python-modules/phonopy/default.nix
+++ b/pkgs/development/python-modules/phonopy/default.nix
@@ -1,5 +1,6 @@
 {
   lib,
+  stdenv,
   buildPythonPackage,
   fetchFromGitHub,
 
@@ -24,14 +25,15 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "phonopy";
-  version = "3.4.0";
+  version = "3.5.1";
   pyproject = true;
+  __structuredAttrs = true;
 
   src = fetchFromGitHub {
     owner = "phonopy";
     repo = "phonopy";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-pCBCZzVSthExY6NhmQKyGj7aFgvHLyztUToYGL4Y3Jo=";
+    hash = "sha256-P5anv0bg+L5dUdmZBECPNLa1AzjB782s8IfZCun7pN4=";
   };
 
   postPatch = ''
@@ -61,6 +63,11 @@ buildPythonPackage (finalAttrs: {
 
   nativeCheckInputs = [ pytestCheckHook ];
 
+  env = lib.optionalAttrs stdenv.hostPlatform.isDarwin {
+    # Prevents 'Fatal Python error: Aborted' on darwin during checkPhase
+    MPLBACKEND = "Agg";
+  };
+
   # prevent pytest from importing local directory
   preCheck = ''
     rm -r phonopy