diff --git a/modules/nf-core/pbmm2/align/main.nf b/modules/nf-core/pbmm2/align/main.nf
index 3233b84df07f..69dc9787f5a3 100644
--- a/modules/nf-core/pbmm2/align/main.nf
+++ b/modules/nf-core/pbmm2/align/main.nf
@@ -23,10 +23,21 @@ process PBMM2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    fasta="${fasta}"
+    if [[ \${fasta} == *.fna ]]; then
+        new_name=\${fasta%.fna}.fa
+        mv \${fasta} \${new_name}
+        fasta=\${new_name}
+    elif [[ \${fasta} == *.fna.gz ]]; then
+        new_name=\${fasta%.fna.gz}.fa.gz
+        mv \${fasta} \${new_name}
+        fasta=\${new_name}
+    fi
+
     pbmm2 \\
         align \\
         $args \\
-        $fasta \\
+        \${fasta} \\
         $bam \\
         ${prefix}.bam \\
         --num-threads ${task.cpus}
diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test b/modules/nf-core/pbmm2/align/tests/fna.nf.test
new file mode 100644
index 000000000000..3a81512116bd
--- /dev/null
+++ b/modules/nf-core/pbmm2/align/tests/fna.nf.test
@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test Process PBMM2_ALIGN"
+    script "../main.nf"
+    process "PBMM2_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbmm2"
+    tag "pbmm2/align"
+
+    test("pbmm2 - bam - fna") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
new file mode 100644
index 000000000000..c3c119baa59c
--- /dev/null
+++ b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
@@ -0,0 +1,28 @@
+{
+    "pbmm2 - bam - fna": {
+        "content": [
+            {
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,f0f615a8a6172a739dfb81e6e08043f4"
+                    ]
+                ],
+                "versions_pbmm2": [
+                    [
+                        "PBMM2_ALIGN",
+                        "pbmm2",
+                        "26.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-06T11:28:10.82763057",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
index 8250bd5826be..4ada87e2eb32 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,f2be1fe20bbccf66afae237452e112cd"
+                        "test.bam:md5,ccb989e67933259d6213ca6236b7971c"
                     ]
                 ],
                 "versions_pbmm2": [
@@ -19,10 +19,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-01T15:03:18.017362993",
+        "timestamp": "2026-07-31T11:02:25.18889907",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.03.4"
+            "nextflow": "26.04.6"
         }
     },
     "pbmm2  - bam - stub": {