diff --git a/modules/nf-core/falint/environment.yml b/modules/nf-core/falint/environment.yml
index 37007a670c5d..a0c5a7534f63 100644
--- a/modules/nf-core/falint/environment.yml
+++ b/modules/nf-core/falint/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::fa-lint=1.0.0
+  - bioconda::fa-lint=1.2.0
diff --git a/modules/nf-core/falint/main.nf b/modules/nf-core/falint/main.nf
index 7e29c34e7f3a..43481f00c935 100644
--- a/modules/nf-core/falint/main.nf
+++ b/modules/nf-core/falint/main.nf
@@ -4,8 +4,8 @@ process FALINT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fa-lint:1.0.0--he881be0_0':
-        'biocontainers/fa-lint:1.0.0--he881be0_0' }"
+        'https://depot.galaxyproject.org/singularity/fa-lint:1.2.0--he881be0_0':
+        'biocontainers/fa-lint:1.2.0--he881be0_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/falint/tests/main.nf.test.snap b/modules/nf-core/falint/tests/main.nf.test.snap
index 127855682720..4f603ec43aee 100644
--- a/modules/nf-core/falint/tests/main.nf.test.snap
+++ b/modules/nf-core/falint/tests/main.nf.test.snap
@@ -15,7 +15,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                    "versions.yml:md5,8fdbf4fa23101f225056b3ac1e3f8bde"
                 ],
                 "error_log": [
                     
@@ -30,27 +30,27 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                    "versions.yml:md5,8fdbf4fa23101f225056b3ac1e3f8bde"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-16T14:55:29.853456"
+        "timestamp": "2025-10-29T10:31:10.693721"
     },
     "sarscov2-gff3-invalid": {
         "content": [
             [
-                "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                "versions.yml:md5,8fdbf4fa23101f225056b3ac1e3f8bde"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-16T15:08:29.434346"
+        "timestamp": "2025-10-29T10:31:20.352025"
     },
     "sarscov2-fasta-valid-stub": {
         "content": [
@@ -68,7 +68,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                    "versions.yml:md5,8fdbf4fa23101f225056b3ac1e3f8bde"
                 ],
                 "error_log": [
                     
@@ -83,14 +83,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6edbfcd6e31e74c05778f1d48191b9f6"
+                    "versions.yml:md5,8fdbf4fa23101f225056b3ac1e3f8bde"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-16T15:08:25.052305"
+        "timestamp": "2025-10-29T10:31:15.422126"
     }
 }
\ No newline at end of file