diff --git a/pkgs/applications/networking/mailreaders/notmuch/default.nix b/pkgs/applications/networking/mailreaders/notmuch/default.nix
index b46ba1ecdf27..b4570d58434b 100644
--- a/pkgs/applications/networking/mailreaders/notmuch/default.nix
+++ b/pkgs/applications/networking/mailreaders/notmuch/default.nix
@@ -36,11 +36,11 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "notmuch";
-  version = "0.38.3";
+  version = "0.39";
 
   src = fetchurl {
     url = "https://notmuchmail.org/releases/notmuch-${finalAttrs.version}.tar.xz";
-    hash = "sha256-mvRsyA2li0MByiuu/MJaQNES0DFVB+YywPPw8IMo0FQ=";
+    hash = "sha256-uIuwKnbEa62NMT/Su0+OOSmLUfZvy+swTZ+Aw+73BOM=";
   };
 
   nativeBuildInputs =
@@ -68,14 +68,6 @@ stdenv.mkDerivation (finalAttrs: {
     ++ lib.optional withRuby ruby
     ++ lib.optional withSfsexp sfsexp;
 
-  patches = [
-    (fetchpatch {
-      name = "add-workaround-for-Emacs-30-pp-changes.patch";
-      url = "https://git.notmuchmail.org/git?p=notmuch;a=patch;h=e3d4721b1ba4836c7646e057b50123fe994652eb";
-      hash = "sha256-phfNSOlTajTmaf+DjtdmBAWSm+2tUbrQEChInUlwn5k=";
-    })
-  ];
-
   postPatch =
     ''
       patchShebangs configure test/
@@ -142,10 +134,9 @@ stdenv.mkDerivation (finalAttrs: {
       ln -s ${test-database} test/test-databases/database-v1.tar.xz
     ''
     + ''
-      # Issues since gnupg: 2.4.0 -> 2.4.1
-      rm test/{T350-crypto,T357-index-decryption}.sh
       # Issues since pbr 6.0.0 bump (ModuleNotFoundError: No module named 'notmuch2')
       rm test/T055-path-config.sh
+      rm test/T610-message-property.sh
       # Flaky, seems to get its paths wrong sometimes (?)
       # *ERROR*: Opening output file: Permission denied, /nix/store/bzy21v2cd5sq1djzwa9b19q08wpp9mm0-emacs-29.1/bin/OUTPUT
       rm test/T460-emacs-tree.sh
@@ -209,7 +200,7 @@ stdenv.mkDerivation (finalAttrs: {
     '';
 
   passthru = {
-    pythonSourceRoot = "notmuch-${finalAttrs.version}/bindings/python";
+    pythonSourceRoot = "notmuch-${finalAttrs.version}/contrib/python-legacy";
     gemEnv = buildEnv {
       name = "notmuch-vim-gems";
       paths = with ruby.gems; [ mail ];