diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5673dd8..12fe219 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,10 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+## [v0.3.3]
 ### Fixed
 - Overwrites in Nextflow config implemented incorrectly
 
+### Changed
+- Updated Medaka to 1.9.1.
+
 ## [v0.3.2]
 ### Fixed
 - Edge case where medaka variant output is unsorted and causes medaka annotate to exit
diff --git a/nextflow.config b/nextflow.config
index c923fba..118a288 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -44,7 +44,7 @@ params {
       common_sha = "sha5fc720674a26bc63a6f31ed186344209175b54b1"
       container_sha = "sha31b8f1a3cf898574ae2b1bb617892126103253a3"
       container_sha_prokka = "sha08669655982fbef7c750c7895e97e100196c4967"
-      container_sha_medaka = "sha6a58ce1871560b8ddaada5cc1dfc51e5c03442e8"
+      container_sha_medaka = "sha492176b6093aa922aae5610f6ad899aacd2c3c7f"
       agent = null
     }
 }
@@ -56,7 +56,7 @@ manifest {
     description     = 'Assembly, variant calling, and annotation of bacterial genomes.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v0.3.2'
+    version         = 'v0.3.3'
 }
 
 epi2melabs {