diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index d496eea8..20ffd094 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -12,3 +12,21 @@ report_section_order:
     order: -1002
 
 export_plots: true
+
+module_order:
+   - fastqc:
+      name: "FastQC (raw)"
+      info: "This section of the report shows FastQC results on the input files."
+      path_filters:
+        - "**/*.raw_fastqc.zip"
+   - fastqc:
+      name: "FastQC (trimmed)"
+      info: "This section of the report shows FastQC results after adapter trimming."
+      path_filters:
+        - "**/*.trim_fastqc.zip"
+   - fastqc:
+      name: "FastQC (deduplicated)"
+      info: "This section of the report shows FastQC results after UMI-based deduplication."
+      path_filters:
+        - "**/*.deduplicated_fastqc.zip"
+
diff --git a/conf/modules.config b/conf/modules.config
index b57e4f92..cbd7d5d1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -74,6 +74,8 @@ process {
         ]
     }
     withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
+        //the prefix is required for multiqc to pickup the files separately from the other fastqc instances
+        ext.prefix =  { "${meta.id}.raw" }
         ext.args = '--quiet'
         publishDir = [
             path: { "${params.outdir}/fastqc/raw" },
@@ -82,6 +84,7 @@ process {
         ]
     }
     withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
+        ext.prefix =  { "${meta.id}.trim" }
         ext.args = '--quiet'
         publishDir = [
             path: { "${params.outdir}/fastqc/trimmed" },
@@ -184,6 +187,16 @@ process {
             )
         ]
     }
+    withName: '.*:DEDUPLICATE_UMIS:FASTQC_DEDUPLICATED' {
+        //the prefix is required for multiqc to pickup the files separately from the other fastqc instances
+        ext.prefix =  { "${meta.id}.deduplicated" }
+        ext.args = '--quiet'
+        publishDir = [
+            path: { "${params.outdir}/fastqc/deduplicated" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
     //
     // MIRTRACE QC
diff --git a/subworkflows/local/umi_dedup.nf b/subworkflows/local/umi_dedup.nf
index 9f65fa8e..2c7b533b 100644
--- a/subworkflows/local/umi_dedup.nf
+++ b/subworkflows/local/umi_dedup.nf
@@ -8,6 +8,7 @@ include { BAM_SORT_STATS_SAMTOOLS             } from '../../subworkflows/nf-core
 include { UMICOLLAPSE                         } from '../../modules/nf-core/umicollapse/main'
 include { SAMTOOLS_BAM2FQ                     } from '../../modules/nf-core/samtools/bam2fq/main'
 include { CAT_CAT                             } from '../../modules/nf-core/cat/cat/main'
+include { FASTQC as FASTQC_DEDUPLICATED        } from '../../modules/nf-core/fastqc/main'
 
 
 workflow DEDUPLICATE_UMIS {
@@ -34,8 +35,12 @@ workflow DEDUPLICATE_UMIS {
 
     ch_dedup_reads = SAMTOOLS_BAM2FQ.out.reads
 
+    FASTQC_DEDUPLICATED(ch_dedup_reads)
+
     emit:
-    reads    = ch_dedup_reads
+    reads = ch_dedup_reads
+    fastqc_html = FASTQC_DEDUPLICATED.out.html
+    fastqc_zip = FASTQC_DEDUPLICATED.out.zip
     indices  = bt_index
     versions = ch_versions
 }
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
index 58a4e8ad..1a7b4e64 100644
--- a/workflows/smrnaseq.nf
+++ b/workflows/smrnaseq.nf
@@ -272,7 +272,9 @@ workflow SMRNASEQ {
         ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(DEDUPLICATE_UMIS.out.fastqc_zip.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(contamination_stats.collect().ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(genome_stats.collect({it[1]}).ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mature_stats.collect({it[1]}).ifEmpty([]))