diff --git a/CHANGELOG.md b/CHANGELOG.md
index 708742c2..ca9f1f5f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#515](https://github.com/nf-core/mag/pull/515) Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
 - [#514](https://github.com/nf-core/mag/pull/514) Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
 
 ### `Dependencies`
diff --git a/conf/modules.config b/conf/modules.config
index 846aa11b..33a19831 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -417,7 +417,7 @@ process {
     // Make sure to keep directory in sync with gunc_qc.nf
     withName: 'GUNC_RUN' {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.id}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -426,7 +426,7 @@ process {
     // Make sure to keep directory in sync with gunc_qc.nf
     withName: 'GUNC_MERGECHECKM' {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.id}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
diff --git a/docs/output.md b/docs/output.md
index c61eb48d..e78d244b 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -561,9 +561,9 @@ If the parameter `--save_checkm_reference` is set, additionally the used the Che
 - `[gunc-database].dmnd`
 - `GUNC/`
   - `raw/`
-    - `[assembler]-[binner]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
   - `checkmmerged/`
-    - `[assembler]-[binner]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
 
 </details>