diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 841ea2fea6c..1efda00abb8 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -17,9 +17,11 @@ process KALLISTOBUSTOOLS_COUNT {
     val   workflow_mode
 
     output:
-    tuple val(meta), path ("*.count")   , emit: count
-    path "versions.yml"                 , emit: versions
-    path "*.count/*/*.mtx"              , emit: matrix //Ensure that kallisto finished and produced outputs
+    tuple val(meta), path ("*.count")                  , emit: count
+    tuple val(meta), path ("*.count/counts_unfiltered"), emit: raw_counts
+    tuple val(meta), path ("*.count/counts_filtered")  , emit: filtered_counts, optional: true
+    path "versions.yml"                                , emit: versions
+    path "*.count/*/*.mtx"                             , emit: matrix //Ensure that kallisto finished and produced outputs
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index 55d5dc6cdc4..d491dffaae3 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -58,6 +58,14 @@ output:
       type: file
       description: kb count output folder
       pattern: "*.{count}"
+  - raw_counts:
+      type: file
+      description: kb raw counts output folder
+      pattern: "*.{count}/counts_unfiltered"
+  - filtered_counts:
+      type: file
+      description: kb filtered counts output folder
+      pattern: "*.{count}/counts_filtered"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
index 3378c3c16fa..6f6b3183328 100644
--- a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
+++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
@@ -15,9 +15,22 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
                 ],
                 "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
+                ],
+                "4": [
                     "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "count": [
@@ -31,10 +44,23 @@
                             ]
                         ]
                     ]
+                ],
+                "filtered_counts": [
+                    
                 ],
                 "matrix": [
                     "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
+                "raw_counts": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
                 ]
@@ -44,7 +70,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-01T15:48:45.775904562"
+        "timestamp": "2024-03-18T11:38:48.980939376"
     },
     "genome.fasta + genome.gtf + '10X3' + 'standard'": {
         "content": [