diff --git a/CHANGELOG.md b/CHANGELOG.md
index ef758c83..2312802c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#438](https://github.com/nf-core/atacseq/issues/438)] - Add `checkIfExists` to file inputs in `PREPARE_GENOME` and prevent S3 access errors during index validation.
 - [[PR #443](https://github.com/nf-core/atacseq/pull/443)] - Updated pipeline template to [nf-core/tools 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2)
 - [[PR #453](https://github.com/nf-core/atacseq/pull/453)] - Updated pipeline template to [nf-core/tools 4.0.3](https://github.com/nf-core/tools/releases/tag/4.0.3)
+- [[PR #454](https://github.com/nf-core/atacseq/pull/454)] - Sort the peak QC plot inputs by file name so that `PLOT_MACS3_QC` and `PLOT_HOMER_ANNOTATEPEAKS` outputs no longer depend on task completion order.
 
 ### Parameters
 
diff --git a/modules/local/plot_homer_annotatepeaks.nf b/modules/local/plot_homer_annotatepeaks.nf
index ef4b1ce6..6b2833a6 100644
--- a/modules/local/plot_homer_annotatepeaks.nf
+++ b/modules/local/plot_homer_annotatepeaks.nf
@@ -23,10 +23,12 @@ process PLOT_HOMER_ANNOTATEPEAKS {
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "annotatepeaks"
+    // Files arrive in task-completion order; sort so sample order in the outputs is reproducible.
+    def anno_list = annos.toSorted { anno -> anno.name }.join(',')
     """
     plot_homer_annotatepeaks.r \\
-        -i ${annos.join(',')} \\
-        -s ${annos.join(',').replaceAll("${suffix}","")} \\
+        -i ${anno_list} \\
+        -s ${anno_list.replaceAll("${suffix}","")} \\
         -p $prefix \\
         $args
 
diff --git a/modules/local/plot_macs3_qc.nf b/modules/local/plot_macs3_qc.nf
index 9ce2edfe..7cf371c2 100644
--- a/modules/local/plot_macs3_qc.nf
+++ b/modules/local/plot_macs3_qc.nf
@@ -21,10 +21,12 @@ process PLOT_MACS3_QC {
     script: // This script is bundled with the pipeline, in nf-core/atacseq/bin/
     def args      = task.ext.args ?: ''
     def peak_type = is_narrow_peak ? 'narrowPeak' : 'broadPeak'
+    // Files arrive in task-completion order; sort so sample order in the outputs is reproducible.
+    def peak_list = peaks.toSorted { peak -> peak.name }.join(',')
     """
     plot_macs3_qc.r \\
-        -i ${peaks.join(',')} \\
-        -s ${peaks.join(',').replaceAll("_peaks.${peak_type}","")} \\
+        -i ${peak_list} \\
+        -s ${peak_list.replaceAll("_peaks.${peak_type}","")} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml