diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index 86b57575e..afe258313 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -19,6 +19,7 @@ Added
 Changed
 -------
 - Remove ``rnaseqc-qc`` from MultiQC report
+- Remove ``rnaseqc-qc`` from RNA-seq workflows
 
 Fixed
 -----
diff --git a/resolwe_bio/processes/workflows/bbduk_salmon_qc.py b/resolwe_bio/processes/workflows/bbduk_salmon_qc.py
index 9eb902eda..e3c8329d4 100644
--- a/resolwe_bio/processes/workflows/bbduk_salmon_qc.py
+++ b/resolwe_bio/processes/workflows/bbduk_salmon_qc.py
@@ -42,7 +42,7 @@ class WorkflowBbdukSalmonQc(Process):
     entity = {
         "type": "sample",
     }
-    version = "4.3.1"
+    version = "4.4.0"
     process_type = "data:workflow:rnaseq:salmon"
     category = "Pipeline"
 
@@ -449,22 +449,4 @@ def run(self, inputs, outputs):
             ]
         }
 
-        # RNA-SeQC tool is initiated only if annotation source is ENSEMBL
-        if inputs.annotation.output.source == "ENSEMBL":
-            input_rnaseqc = {
-                "alignment": alignment_qc,
-                "annotation": inputs.annotation,
-                "strand_detection_options": {
-                    "stranded": "auto",
-                    "cdna_index": inputs.salmon_index,
-                    "n_reads": 5000000,
-                },
-            }
-            rnaseqc = Data.create(
-                process=BioProcess.get_latest(slug="rnaseqc-qc"),
-                input=input_rnaseqc,
-                name=f"RNA-SeQC QC report ({inputs.reads.name})",
-            )
-            input_multiqc["data"].append(rnaseqc)
-
         Data.create(process=BioProcess.get_latest(slug="multiqc"), input=input_multiqc)
diff --git a/resolwe_bio/processes/workflows/bbduk_star.py b/resolwe_bio/processes/workflows/bbduk_star.py
index 3f9c7c138..1b95621d8 100644
--- a/resolwe_bio/processes/workflows/bbduk_star.py
+++ b/resolwe_bio/processes/workflows/bbduk_star.py
@@ -41,7 +41,7 @@ class WorkflowSTAR(Process):
         "expression-engine": "jinja",
     }
     data_name = "{{ reads|name|default('?') }}"
-    version = "1.4.0"
+    version = "1.5.0"
     entity = {
         "type": "sample",
     }
@@ -731,24 +731,4 @@ def run(self, inputs, outputs):
             "advanced": {"dirs": True, "config": True},
         }
 
-        # RNA-SeQC tool is initiated only if annotation source is ENSEMBL
-        if inputs.annotation.output.source == "ENSEMBL":
-            input_rnaseqc = {
-                "alignment": alignment_downsampled,
-                "annotation": inputs.annotation,
-                "strand_detection_options": {"stranded": inputs.assay_type},
-            }
-
-            if inputs.cdna_index:
-                input_rnaseqc["strand_detection_options"][
-                    "cdna_index"
-                ] = inputs.cdna_index
-
-            rnaseqc = Data.create(
-                process=BioProcess.get_latest(slug="rnaseqc-qc"),
-                input=input_rnaseqc,
-                name=f"RNA-SeQC QC report ({inputs.reads.name})",
-            )
-            input_multiqc["data"].append(rnaseqc)
-
         Data.create(process=BioProcess.get_latest(slug="multiqc"), input=input_multiqc)
diff --git a/resolwe_bio/processes/workflows/bbduk_star_featurecounts_qc.py b/resolwe_bio/processes/workflows/bbduk_star_featurecounts_qc.py
index 635022261..1030800ce 100644
--- a/resolwe_bio/processes/workflows/bbduk_star_featurecounts_qc.py
+++ b/resolwe_bio/processes/workflows/bbduk_star_featurecounts_qc.py
@@ -46,7 +46,7 @@ class WorkflowBBDukStarFcQC(Process):
     entity = {
         "type": "sample",
     }
-    version = "6.2.0"
+    version = "6.3.0"
     process_type = "data:workflow:rnaseq:featurecounts:qc"
     category = "Pipeline"
 
@@ -764,24 +764,4 @@ def run(self, inputs, outputs):
             "advanced": {"dirs": True, "config": True},
         }
 
-        # RNA-SeQC tool is initiated only if annotation source is ENSEMBL
-        if inputs.annotation.output.source == "ENSEMBL":
-            input_rnaseqc = {
-                "alignment": alignment_downsampled,
-                "annotation": inputs.annotation,
-                "strand_detection_options": {"stranded": inputs.assay_type},
-            }
-
-            if inputs.cdna_index:
-                input_rnaseqc["strand_detection_options"][
-                    "cdna_index"
-                ] = inputs.cdna_index
-
-            rnaseqc = Data.create(
-                process=BioProcess.get_latest(slug="rnaseqc-qc"),
-                input=input_rnaseqc,
-                name=f"RNA-SeQC QC report ({inputs.reads.name})",
-            )
-            input_multiqc["data"].append(rnaseqc)
-
         Data.create(process=BioProcess.get_latest(slug="multiqc"), input=input_multiqc)