diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0a2c0010f..33b7da3e7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -57,6 +57,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1730](https://github.com/nf-core/rnaseq/pull/1730) - Bump Nextflow from 25.04.0 to 25.04.3 in CI to fix `conda create --mkdir` failure ([nextflow-io/nextflow#5947](https://github.com/nextflow-io/nextflow/issues/5947))
 - [PR #1734](https://github.com/nf-core/rnaseq/pull/1734) - Compose `test_prokaryotic` profile on `prokaryotic` to remove duplicated settings
 - [PR #1735](https://github.com/nf-core/rnaseq/pull/1735) - Code quality improvements: replace opaque tuple indexing with named destructuring, rename `ch_dummy_file`, move metro map docs, align GPU CI workflow with other workflows
+- [PR #1736](https://github.com/nf-core/rnaseq/pull/1736) - Load prokaryotic config in nf-test instead of duplicating params in each test
 
 ### Parameters
 
diff --git a/tests/prokaryotic.nf.test b/tests/prokaryotic.nf.test
index 46accfe92..c9cd7bb40 100644
--- a/tests/prokaryotic.nf.test
+++ b/tests/prokaryotic.nf.test
@@ -2,6 +2,7 @@ nextflow_pipeline {
 
     name "Test pipeline with prokaryotic settings"
     script "../main.nf"
+    config "../conf/prokaryotic.config"
     tag "pipeline"
     tag "prokaryotic"
 
@@ -21,23 +22,15 @@ nextflow_pipeline {
                 transcript_fasta = null
                 additional_fasta = null
 
-                // Prokaryotic-specific settings
-                prokaryotic = true
-                gffread_transcript_fasta = true
+                // Override aligner (prokaryotic profile defaults to bowtie2_salmon)
                 aligner = 'star_salmon'
-                featurecounts_feature_type = 'CDS'
 
-                // Skip eukaryote-specific QC tools
-                skip_rseqc = true
-                skip_dupradar = true
-                skip_qualimap = true
+                // Skip steps not needed for minimal testing
+                skip_bbsplit    = true
+                skip_preseq     = true
                 skip_biotype_qc = true
-                skip_deseq2_qc = true
-
-                // Skip unnecessary steps for faster testing
-                skip_bbsplit = true
-                skip_preseq = true
-                pseudo_aligner = null
+                skip_deseq2_qc  = true
+                pseudo_aligner  = null
                 min_trimmed_reads = 0
             }
         }
@@ -77,23 +70,15 @@ nextflow_pipeline {
                 transcript_fasta = null
                 additional_fasta = null
 
-                // Prokaryotic-specific settings
-                prokaryotic = true
-                gffread_transcript_fasta = true
+                // Override aligner (prokaryotic profile defaults to bowtie2_salmon)
                 aligner = 'star_salmon'
-                featurecounts_feature_type = 'CDS'
 
-                // Skip eukaryote-specific QC tools
-                skip_rseqc = true
-                skip_dupradar = true
-                skip_qualimap = true
+                // Skip steps not needed for minimal testing
+                skip_bbsplit    = true
+                skip_preseq     = true
                 skip_biotype_qc = true
-                skip_deseq2_qc = true
-
-                // Skip unnecessary steps for faster testing
-                skip_bbsplit = true
-                skip_preseq = true
-                pseudo_aligner = null
+                skip_deseq2_qc  = true
+                pseudo_aligner  = null
                 min_trimmed_reads = 0
             }
         }
@@ -135,23 +120,12 @@ nextflow_pipeline {
                 transcript_fasta = null
                 additional_fasta = null
 
-                // Prokaryotic-specific settings
-                gffread_transcript_fasta = true
-                aligner = 'bowtie2_salmon'
-                skip_bigwig = true
-                featurecounts_feature_type = 'CDS'
-
-                // Skip eukaryote-specific QC tools
-                skip_rseqc = true
-                skip_dupradar = true
-                skip_qualimap = true
+                // Skip steps not needed for minimal testing
+                skip_bbsplit    = true
+                skip_preseq     = true
                 skip_biotype_qc = true
-                skip_deseq2_qc = true
-
-                // Skip unnecessary steps for faster testing
-                skip_bbsplit = true
-                skip_preseq = true
-                pseudo_aligner = null
+                skip_deseq2_qc  = true
+                pseudo_aligner  = null
                 min_trimmed_reads = 0
             }
         }
@@ -191,23 +165,12 @@ nextflow_pipeline {
                 transcript_fasta = null
                 additional_fasta = null
 
-                // Prokaryotic-specific settings
-                gffread_transcript_fasta = true
-                aligner = 'bowtie2_salmon'
-                skip_bigwig = true
-                featurecounts_feature_type = 'CDS'
-
-                // Skip eukaryote-specific QC tools
-                skip_rseqc = true
-                skip_dupradar = true
-                skip_qualimap = true
+                // Skip steps not needed for minimal testing
+                skip_bbsplit    = true
+                skip_preseq     = true
                 skip_biotype_qc = true
-                skip_deseq2_qc = true
-
-                // Skip unnecessary steps for faster testing
-                skip_bbsplit = true
-                skip_preseq = true
-                pseudo_aligner = null
+                skip_deseq2_qc  = true
+                pseudo_aligner  = null
                 min_trimmed_reads = 0
             }
         }
diff --git a/tests/prokaryotic.nf.test.snap b/tests/prokaryotic.nf.test.snap
index 8dbc70bc4..c297ea756 100644
--- a/tests/prokaryotic.nf.test.snap
+++ b/tests/prokaryotic.nf.test.snap
@@ -1,14 +1,8 @@
 {
     "Params: --aligner star_salmon --prokaryotic": {
         "content": [
-            58,
+            46,
             {
-                "BEDTOOLS_GENOMECOV_FW": {
-                    "bedtools": "2.31.1"
-                },
-                "BEDTOOLS_GENOMECOV_REV": {
-                    "bedtools": "2.31.1"
-                },
                 "CUSTOM_TX2GENE": {
                     "python": "3.10.4"
                 },
@@ -82,12 +76,6 @@
                 "TXIMETA_TXIMPORT": {
                     "bioconductor-tximeta": "1.20.1"
                 },
-                "UCSC_BEDCLIP": {
-                    "ucsc": 377
-                },
-                "UCSC_BEDGRAPHTOBIGWIG": {
-                    "ucsc": 469
-                },
                 "UNTAR_SALMON_INDEX": {
                     "untar": 1.34
                 }
@@ -347,11 +335,6 @@
                 "star_salmon/SALM_REP2/logs/salmon_quant.log",
                 "star_salmon/SALM_REP2/quant.genes.sf",
                 "star_salmon/SALM_REP2/quant.sf",
-                "star_salmon/bigwig",
-                "star_salmon/bigwig/SALM_REP1.forward.bigWig",
-                "star_salmon/bigwig/SALM_REP1.reverse.bigWig",
-                "star_salmon/bigwig/SALM_REP2.forward.bigWig",
-                "star_salmon/bigwig/SALM_REP2.reverse.bigWig",
                 "star_salmon/log",
                 "star_salmon/log/SALM_REP1.Log.final.out",
                 "star_salmon/log/SALM_REP1.Log.out",