diff --git a/CHANGELOG.md b/CHANGELOG.md
index 983257e47..bf40d1f65 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#1012](https://github.com/nf-core/mag/pull/1012) - Prevent adapter trimming with Porechop on PacBio reads (by @dialvarezs)
 - [#1011](https://github.com/nf-core/mag/pull/1011) - Fix issue making CheckM2 running only for one sample per run (by @dialvarezs)
+- [#1017](https://github.com/nf-core/mag/pull/1017) - Prevent ALE running on long read assemblies when a sample has both LR and SR data (reported by @jfy133, fix by @dialvarezs)
 
 ### `Dependencies`
 
diff --git a/workflows/mag.nf b/workflows/mag.nf
index 3d671db4f..d70d890a5 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -275,12 +275,8 @@ workflow MAG {
     */
 
     if (!params.skip_ale) {
-        ch_shortread_assemblies_for_ale = ch_assemblies.filter { meta, _assembly ->
-            meta.sr_platform != null && meta.sr_platform != []
-        }
-
         ch_ale_input = BINNING_PREPARATION.out.grouped_mappings
-            .join(ch_shortread_assemblies_for_ale, by: 0)
+            .join(ch_shortread_assemblies, by: 0)
             .map { meta, _contigs, bams, _bais, assembly ->
                 // Try to find the BAM where reads came from the same sample as the assembly (co-binning may include multiple BAMs)
                 // If none matches (coassembly), take the first one after sorting for determinism