diff --git a/subworkflows/local/mtx_conversion.nf b/subworkflows/local/mtx_conversion.nf
index 55541f18..98e49a2e 100644
--- a/subworkflows/local/mtx_conversion.nf
+++ b/subworkflows/local/mtx_conversion.nf
@@ -14,6 +14,16 @@ workflow MTX_CONVERSION {
     main:
         ch_versions = Channel.empty()
 
+        // Cellranger module output contains too many files which cause path collisions, we filter to the ones we need.
+        // Keeping backwards compatibility with cellranger-arc.
+        // TODO: Adapt cellranger-arc subworkflow like cellranger to remove this snippet here.
+        if (params.aligner in [ 'cellrangerarc' ]) {
+            mtx_matrices = mtx_matrices.map { meta, mtx_files ->
+                    [ meta, mtx_files.findAll { it.toString().contains("filtered_feature_bc_matrix") } ]
+                }
+                .filter { meta, mtx_files -> mtx_files } // Remove any that are missing the relevant files
+        }
+
         //
         // Convert matrix to h5ad
         //