diff --git a/CHANGELOG.md b/CHANGELOG.md
index 895d66af8..c5066a4db 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -151,6 +151,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#650](https://github.com/nf-core/sarek/pull/650) - Fix intervals checks
 - [#654](https://github.com/nf-core/sarek/pull/654) - Allow any step but annotation to start from BAM files
 - [#658](https://github.com/nf-core/sarek/pull/658) - Fix split fastq names in multiqc-report
+- [#666](https://github.com/nf-core/sarek/pull/666) - Simplify multiqc config channel input
 
 ### Deprecated
 
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 750d06bbb..91771c4e3 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -973,13 +973,12 @@ workflow SAREK {
         ch_workflow_summary = Channel.value(workflow_summary)
 
         ch_multiqc_files =  Channel.empty().mix(ch_version_yaml,
-                                            Channel.from(ch_multiqc_config),
-                                            ch_multiqc_custom_config.collect().ifEmpty([]),
                                             ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'),
-                                            ch_reports.collect()
-                                            )
+                                            ch_reports.collect())
 
-        MULTIQC(ch_multiqc_files.collect(), ch_multiqc_config)
+        ch_multiqc_configs = Channel.from(ch_multiqc_config).mix(ch_multiqc_custom_config).ifEmpty([])
+
+        MULTIQC(ch_multiqc_files.collect(), ch_multiqc_configs.collect())
         multiqc_report = MULTIQC.out.report.toList()
     }
 }