diff --git a/CHANGELOG.md b/CHANGELOG.md
index a45025384..15922dcac 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -114,6 +114,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1355](https://github.com/nf-core/rnaseq/pull/1355) - Make all curves on subway map better looking, and all lines now have the same width
 - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc
 - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests
+- [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround
 
 ### Parameters
 
diff --git a/modules.json b/modules.json
index a01086438..bc800fd45 100644
--- a/modules.json
+++ b/modules.json
@@ -92,7 +92,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "878d2adbb911aa6e15c06a4d1e93d01bd6f26c74",
+                        "git_sha": "fb387b16025333f6d66b88d6c48c3719f47b1637",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index 0eb9d9c90..a31464c97 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.24
+  - bioconda::multiqc=1.24.1
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 9790c23cf..d5365800d 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.24--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.24--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index ef35f6d57..83fa080c8 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,0c5c5c2a79011c26b34b0b0e80b7c8e2"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
@@ -17,7 +17,7 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,0c5c5c2a79011c26b34b0b0e80b7c8e2"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
@@ -29,7 +29,7 @@
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,0c5c5c2a79011c26b34b0b0e80b7c8e2"
+                "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760"
             ]
         ],
         "meta": {
diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
index 75367a073..49d3939e2 100644
--- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml
+++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -11,13 +11,13 @@ report_section_order:
   fail_strand_check-module:
     order: 5001
   # Preprocessing and pre-alignment QC
-  fastqc:
+  fastqc_raw:
     order: 4004
   cutadapt:
     order: 4003
   fastp:
     order: 4003
-  fastqc-1:
+  fastqc_trimmed:
     order: 4002
   # Alignment
   star:
@@ -98,6 +98,7 @@ run_modules:
 
 module_order:
   - fastqc:
+      anchor: "fastqc_raw"
       name: "FastQC (raw)"
       info: "This section of the report shows FastQC results before adapter trimming."
       path_filters:
@@ -105,6 +106,7 @@ module_order:
   - cutadapt
   - fastp
   - fastqc:
+      anchor: "fastqc_trimmed"
       name: "FastQC (trimmed)"
       info: "This section of the report shows FastQC results after adapter trimming."
       path_filters: