diff --git a/recipes/mzmine/build.patch b/recipes/mzmine/build.patch
index dcfd2832aa3ff..81685331a8262 100644
--- a/recipes/mzmine/build.patch
+++ b/recipes/mzmine/build.patch
@@ -1,9 +1,9 @@
 # - without installerType set jpackage tries to create rpm and deb
 #   we don't need any of them, but I did not find a way to disable
 #   both. so we leave rpm which is available in conda (spkg isn't)
-diff -ruN mzmine3-3.6.0-org/build.gradle mzmine3-3.6.0/build.gradle
---- mzmine3-3.6.0-org/build.gradle	2023-06-21 14:39:23.000000000 +0200
-+++ mzmine3-3.6.0/build.gradle	2023-06-22 17:53:22.239977816 +0200
+diff -ruN mzmine3-3.9.0-org/build.gradle mzmine3-3.9.0/build.gradle
+--- mzmine3-3.9.0-org/build.gradle	2023-06-21 14:39:23.000000000 +0200
++++ mzmine3-3.9.0/build.gradle	2023-06-22 17:53:22.239977816 +0200
 @@ -392,7 +392,7 @@
          if (OperatingSystem.current().isLinux()) {
              // leave installer type empty to generate all that match
@@ -14,15 +14,15 @@ diff -ruN mzmine3-3.6.0-org/build.gradle mzmine3-3.6.0/build.gradle
              imageOptions = ["--icon", "src/main/resources/MZmineIcon.png"]
              installerOptions = ["--linux-shortcut",
 # version is set wrong https://github.com/mzmine/mzmine3/issues/1405
-diff -ruN mzmine3-3.6.0-org/src/main/resources/mzmineversion.properties mzmine3-3.6.0/src/main/resources/mzmineversion.properties
---- mzmine3-3.6.0-org/src/main/resources/mzmineversion.properties	2023-06-21 14:39:23.000000000 +0200
-+++ mzmine3-3.6.0/src/main/resources/mzmineversion.properties	2023-06-22 19:14:12.455764423 +0200
+diff -ruN mzmine3-3.9.0-org/src/main/resources/mzmineversion.properties mzmine3-3.9.0/src/main/resources/mzmineversion.properties
+--- mzmine3-3.9.0-org/src/main/resources/mzmineversion.properties	2023-06-21 14:39:23.000000000 +0200
++++ mzmine3-3.9.0/src/main/resources/mzmineversion.properties	2023-06-22 19:14:12.455764423 +0200
 @@ -3,6 +3,6 @@
  version.buildmeta=
  version.major=3
- version.minor=6
+ version.minor=9
 -version.patch=1
 +version.patch=0
  version.prerelease=
--version.semver=3.6.1
-+version.semver=3.6.0
+-version.semver=3.9.1
++version.semver=3.9.0
diff --git a/recipes/mzmine/meta.yaml b/recipes/mzmine/meta.yaml
index 74db59cb8c9e1..84b0ebd88566b 100644
--- a/recipes/mzmine/meta.yaml
+++ b/recipes/mzmine/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "3.6.0" %}
+{% set version = "3.9.0" %}
 
 package:
   name: mzmine
@@ -7,10 +7,12 @@ package:
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('mzmine', max_pin='x') }}
 
 source:
   - url: https://github.com/mzmine/mzmine3/archive/refs/tags/v{{ version }}.tar.gz
-    sha256: 0446c3e9c0fa777904fcb1354a57aaf611ef5718042930fd8c243c9245157ef2
+    sha256: ca0c206f63201e82d6e7e337c373449e69b4510dbd51adec8f13bed519e07257
     patches:
       - "build.patch"