diff --git a/CLAUDE.md b/CLAUDE.md
index 73d3ae6..eccd6b0 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -140,7 +140,7 @@ Expected CSV format with header:
 
 ### Error Handling
 
-- `SRATOOLS_FASTERQDUMP` has retry logic: falls back from `fasterq-dump` to `fastq-dump` on failure
+- `SRATOOLS_FASTERQDUMP` has retry logic: falls back from `fasterq-dump` to `fastq-dump --split-3` on failure, keeping the same `_1`/`_2` mate layout
 - `SRATOOLS_PREFETCH` uses retry template with exponential backoff
 - Maximum 2 concurrent processes (`maxForks = 2`)
 - `SKETCH_REFERENCE` fails loudly (rather than producing a bogus genome size) if
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index 9508e67..ac71782 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -24,7 +24,8 @@ process SRATOOLS_FASTERQDUMP {
     task.ext.when == null || task.ext.when
 
     script:
-    def sraCommand = task.attempt > 1 ? "fastq-dump" : "fasterq-dump";
+    // fastq-dump does not split mates by default; --split-3 matches fasterq-dump's output layout.
+    def sraCommand = task.attempt > 1 ? "fastq-dump --split-3" : "fasterq-dump";
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"