diff --git a/CHANGELOG.md b/CHANGELOG.md
index d5c45983f..c3ec4abac 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,11 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Special thanks to the following for their contributions to the release:
 
 - [Elad Herzog](https://github.com/EladH1)
+- [Emily Miyoshi](https://github.com/emilymiyoshi)
 
 ### Enhancements and fixes
 
 - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
 - [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
+- [PR #1620](https://github.com/nf-core/rnaseq/pull/1620) - Fix bigwig strand labeling for reverse-stranded libraries ([#1591](https://github.com/nf-core/rnaseq/issues/1591))
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index d3a3ded0c..90bf218c3 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/main.nf
@@ -499,6 +499,7 @@ workflow RNASEQ {
 
     //
     // MODULE: Genome-wide coverage with BEDTools
+    // Note: Strand parameters are conditional on library strandedness (see nextflow.config)
     //
     if (!params.skip_bigwig) {
 
diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config
index 7bd96fc31..84c945cd9 100644
--- a/workflows/rnaseq/nextflow.config
+++ b/workflows/rnaseq/nextflow.config
@@ -335,7 +335,7 @@ if (!params.skip_bigwig) {
     process {
         withName: 'BEDTOOLS_GENOMECOV_FW' {
             ext.prefix = { meta.strandedness == 'reverse' ? meta.id + '.reverse' :  meta.id + '.forward' }
-            ext.args   = '-split -du -strand + -bg'
+            ext.args   = { meta.strandedness == 'reverse' ? '-split -du -strand - -bg' : '-split -du -strand + -bg' }
             publishDir = [
                 enabled: false
             ]
@@ -343,7 +343,7 @@ if (!params.skip_bigwig) {
 
         withName: 'BEDTOOLS_GENOMECOV_REV' {
             ext.prefix = { meta.strandedness == 'reverse' ? meta.id + '.forward' :  meta.id + '.reverse' }
-            ext.args   = '-split -du -strand - -bg'
+            ext.args   = { meta.strandedness == 'reverse' ? '-split -du -strand + -bg' : '-split -du -strand - -bg' }
             publishDir = [
                 enabled: false
             ]