diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index 42aa09c9f5b..1811d7457ff 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -9,8 +9,10 @@ process CELLRANGER_COUNT {
     path  reference
 
     output:
-    tuple val(meta), path("**/outs/**"), emit: outs
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("**/outs/**")                          , emit: outs
+    tuple val(meta), path("**/outs/filtered_feature_bc_matrix**"), emit: filtered
+    tuple val(meta), path("**/outs/raw_feature_bc_matrix**")     , emit: raw
+    path "versions.yml"                                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,7 +34,11 @@ process CELLRANGER_COUNT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p "${prefix}/outs/"
+    mkdir -p "${prefix}/outs/filtered_feature_bc_matrix"
+    mkdir -p "${prefix}/outs/raw_feature_bc_matrix"
     echo "$prefix" > ${prefix}/outs/fake_file.txt
+    echo "$prefix" > ${prefix}/outs/filtered_feature_bc_matrix/fake_file.txt
+    echo "$prefix" > ${prefix}/outs/raw_feature_bc_matrix/fake_file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml
index 1f1768a857b..562449769b8 100644
--- a/modules/nf-core/cellranger/count/meta.yml
+++ b/modules/nf-core/cellranger/count/meta.yml
@@ -40,6 +40,14 @@ output:
       type: file
       description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
       pattern: "${meta.id}/outs/*"
+  - filtered:
+      type: file
+      description: Files containing the filtered outputs of Cell Ranger.
+      pattern: "**/outs/filtered_feature_bc_matrix**"
+  - raw:
+      type: file
+      description: Files containing the raw outputs of Cell Ranger.
+      pattern: "**/outs/raw_feature_bc_matrix**"
   - versions:
       type: file
       description: File containing software version
diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test.snap b/modules/nf-core/cellranger/count/tests/main.nf.test.snap
index 7eafafd02e9..edfb304b733 100644
--- a/modules/nf-core/cellranger/count/tests/main.nf.test.snap
+++ b/modules/nf-core/cellranger/count/tests/main.nf.test.snap
@@ -33,13 +33,61 @@
                             "single_end": false,
                             "strandedness": "auto"
                         },
-                        "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
+                        [
+                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
+                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
+                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
+                        ]
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "test_10x",
+                            "single_end": false,
+                            "strandedness": "auto"
+                        },
+                        "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test_10x",
+                            "single_end": false,
+                            "strandedness": "auto"
+                        },
+                        "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
+                    ]
+                ],
+                "3": [
                     "versions.yml:md5,30cee1a9146b01c48d9b1db6bbe813b6"
                 ],
+                "filtered": [
+                    [
+                        {
+                            "id": "test_10x",
+                            "single_end": false,
+                            "strandedness": "auto"
+                        },
+                        "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
+                    ]
+                ],
                 "outs": [
+                    [
+                        {
+                            "id": "test_10x",
+                            "single_end": false,
+                            "strandedness": "auto"
+                        },
+                        [
+                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
+                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d",
+                            "fake_file.txt:md5,0d98223c768861fd6af96f00148dbb8d"
+                        ]
+                    ]
+                ],
+                "raw": [
                     [
                         {
                             "id": "test_10x",
@@ -58,6 +106,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-05T17:16:12.322822411"
+        "timestamp": "2024-03-18T11:41:17.258523741"
     }
 }
\ No newline at end of file