diff --git a/srcpkgs/notmuch/notmuch-python3.INSTALL.msg b/srcpkgs/notmuch/notmuch-python3.INSTALL.msg
new file mode 100644
index 00000000000..5e36b54b501
--- /dev/null
+++ b/srcpkgs/notmuch/notmuch-python3.INSTALL.msg
@@ -0,0 +1,3 @@
+The legacy python bindings in this package have been deprecated and
+are unsupported by notmuch, and will likely be phased out in upcoming
+releases. Please switch to the new cffi bindings in python3-notmuch2.
diff --git a/srcpkgs/notmuch/template b/srcpkgs/notmuch/template
index 52648d3305d..d35db7d9b30 100644
--- a/srcpkgs/notmuch/template
+++ b/srcpkgs/notmuch/template
@@ -1,14 +1,15 @@
 # Template file for 'notmuch'
 pkgname=notmuch
-version=0.38
-revision=4
+version=0.39
+revision=1
 build_style=configure
 build_helper=python3
 configure_args="--prefix=/usr
  --emacslispdir=/usr/share/emacs/site-lisp/notmuch
  --emacsetcdir=/usr/share/emacs/site-lisp/notmuch"
 hostmakedepends="perl pkg-config python3-Sphinx python3-devel texinfo
- desktop-file-utils emacs gnupg python3-setuptools python3-cffi"
+ desktop-file-utils emacs gnupg python3-setuptools python3-cffi
+ python3-build python3-installer doxygen"
 makedepends="bash-completion gmime3-devel talloc-devel xapian-core-devel
  python3-cffi"
 depends="gmime3>=3.2.7"
@@ -20,11 +21,13 @@ license="GPL-3.0-or-later"
 homepage="https://notmuchmail.org"
 distfiles="https://notmuchmail.org/releases/notmuch-${version}.tar.xz
  https://notmuchmail.org/releases/test-databases/database-v1.tar.xz"
-checksum="a17901adbe43f481a6bf53c15a2a20268bc8dc7ad5ccf685a0d17c1456dbaf6e
+checksum="b88bb02a76c46bad8d313fd2bb4f8e39298b51f66fcbeb304d9f80c3eef704e3
  4299e051b10e1fa7b33ea2862790a09ebfe96859681804e5251e130f800e69d2"
 skip_extraction="database-v1.tar.xz"
 replaces="notmuch-emacs>=0"
 
+make_check="ci-skip" # dtach based tests fail in CI due to no pty
+
 # Not a real conflicts, but this package is broken with gpgme 1.13.1-
 # gpgme is optional dependency
 conflicts="gpgme<1.14.0_1"
@@ -39,10 +42,10 @@ fi
 do_build() {
 	make ${makejobs}
 	make -C contrib/notmuch-mutt
-	cd ${wrksrc}/bindings/python
-	python3 setup.py build --build-base=build
 	cd ${wrksrc}/bindings/python-cffi
-	python3 setup.py build --build-base=build
+	python -m build --wheel --skip-dependency-check --no-isolation
+	cd ${wrksrc}/contrib/python-legacy
+	python -m build --wheel --skip-dependency-check --no-isolation
 }
 
 do_check() {
@@ -51,17 +54,20 @@ do_check() {
 		# Seem like gpgconf's problem,
 		# mutt on musl also have problems with smime
 		NOTMUCH_SKIP_TESTS="smime.3 smime.5"
+		# bad regex test fails on musl
+		NOTMUCH_SKIP_TESTS+=" as-text.10"
 	else
 		# This test run under gdb is problematic
 		NOTMUCH_SKIP_TESTS="count.14"
 	fi
 	# libconfig because of fqdn
-	# we don't ship python-cffi
-	NOTMUCH_SKIP_TESTS+=" libconfig python-cffi"
+	NOTMUCH_SKIP_TESTS+=" libconfig"
 	NOTMUCH_SKIP_TESTS+=" crypto index-decryption"
 	if [ $(id -u) = 0 ]; then
 		NOTMUCH_SKIP_TESTS+=" new.36 new.39 tagging.25"
 	fi
+	# fails due to our gmime configure patches
+	NOTMUCH_SKIP_TESTS+=" smime.4"
 	export NOTMUCH_SKIP_TESTS
 	make test
 }
@@ -84,6 +90,7 @@ libnotmuch-devel_package() {
 	pkg_install() {
 		vmove usr/include
 		vmove usr/lib/*.so
+		vmove usr/share/man/man3
 	}
 }
 
@@ -99,21 +106,19 @@ notmuch-mutt_package() {
 
 notmuch-python3_package() {
 	depends="libnotmuch python3"
-	short_desc+=" - Python 3 bindings"
+	short_desc+=" - Python 3 bindings (legacy)"
 	pkg_install() {
-		cd ${wrksrc}/bindings/python
-		python3 setup.py build --build-base=build \
-			install --prefix=/usr --root=${PKGDESTDIR}
+		cd ${wrksrc}/contrib/python-legacy
+		python -m installer --destdir="$PKGDESTDIR" dist/*.whl
 	}
 }
 
 python3-notmuch2_package() {
-	depends="libnotmuch python3"
+	depends="libnotmuch python3 python3-cffi"
 	short_desc+=" - Python 3 cffi bindings"
 	pkg_install() {
 		cd ${wrksrc}/bindings/python-cffi
-		python3 setup.py build --build-base=build \
-			install --prefix=/usr --root=${PKGDESTDIR}
+		python -m installer --destdir="$PKGDESTDIR" dist/*.whl
 	}
 }