diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
index 564299abc5..38685f1d07 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
@@ -3,6 +3,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
         process {
             withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
                 ext.args   = '--quiet'
+                ext.prefix = { "${meta.id}_raw" }
                 publishDir = [
                     path: { "${params.outdir}/fastqc/raw" },
                     mode: params.publish_dir_mode,
@@ -12,6 +13,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
 
             withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
                 ext.args   = '--quiet'
+                ext.prefix = { "${meta.id}_trimmed" }
                 publishDir = [
                     path: { "${params.outdir}/fastqc/trim" },
                     mode: params.publish_dir_mode,
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
index 63a1eee09e..c3937d2c40 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
@@ -3,6 +3,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
         process {
             withName: '.*:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
                 ext.args   = '--quiet'
+                ext.prefix = { "${meta.id}_raw" }
                 publishDir = [
                     path: { "${params.outdir}/fastqc/raw" },
                     mode: params.publish_dir_mode,
diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
index 91a858775b..9b5facaa49 100644
--- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml
+++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -50,7 +50,7 @@ module_order:
       anchor: "fastqc_raw"
       info: "This section of the report shows FastQC results before adapter trimming."
       path_filters:
-        - "**/raw/*.zip"
+        - "*_raw_fastqc.zip"
   - cutadapt
   - fastp
   - fastqc:
@@ -58,7 +58,7 @@ module_order:
       anchor: "fastqc_trimmed"
       info: "This section of the report shows FastQC results after adapter trimming."
       path_filters:
-        - "**/trim/*.zip"
+        - "*_trimmed_fastqc.zip"
 
 # Don't show % Dups in the General Stats table (we have this from Picard)
 table_columns_visible: