diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6a61e5e0a..3c386d31d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1624](https://github.com/nf-core/rnaseq/pull/1624) - Document RSeQC inner_distance limitation for genomes with large chromosomes (>500 Mb), such as plant genomes
 - [PR #1625](https://github.com/nf-core/rnaseq/pull/1625) - Add documentation warning about Qualimap read counting bug ([#1273](https://github.com/nf-core/rnaseq/issues/1273))
 - [PR #1628](https://github.com/nf-core/rnaseq/pull/1628) - Template update for nf-core/tools v3.5.1
+- [PR #1631](https://github.com/nf-core/rnaseq/pull/1631) - Fix bbsplit index staging by using symlinks instead of full copy
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 
diff --git a/modules.json b/modules.json
index 9a7228cfa..3c4ea02bf 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "fa1477128e0ff24675c8f56d6c334fcc323025c4",
+                        "git_sha": "6da7216c83d9d885bdeb7aef1bcb9b51a90f370b",
                         "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
                     },
                     "bedtools/genomecov": {
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index 2deebbec7..c755bb718 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -68,15 +68,16 @@ process BBMAP_BBSPLIT {
     }
     """
 
-    # If using a pre-built index, copy it to avoid modifying input files in place,
-    # then fix timestamps. When we stage in the index files the time stamps get
-    # disturbed, which bbsplit doesn't like. Fix the time stamps in its summaries.
-    # This needs to be done via Java to match what bbmap does.
+    # If using a pre-built index, create writable structure: symlink all files except
+    # summary.txt (which we copy to modify). When we stage in the index files the time
+    # stamps get disturbed, which bbsplit doesn't like. Fix the time stamps in summaries.
     if [ "$use_index" == "true" ]; then
-        cp -rL input_index index_writable
-
-        for summary_file in \$(find index_writable/ref/genome -name summary.txt); do
-            # Extract the path from summary.txt and update it to point to index_writable
+        find input_index/ref -type f | while read -r f; do
+            target="index_writable/\${f#input_index/}"
+            mkdir -p "\$(dirname "\$target")"
+            [[ \$(basename "\$f") == "summary.txt" ]] && cp "\$f" "\$target" || ln -s "\$(realpath "\$f")" "\$target"
+        done
+        find index_writable/ref/genome -name summary.txt | while read -r summary_file; do
             src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/ref/|index_writable/ref/|')
             mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
             sed -e 's|bbsplit_index/ref|index_writable/ref|' -e "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
@@ -95,14 +96,11 @@ process BBMAP_BBSPLIT {
         $args 2>| >(tee ${prefix}.log >&2)
 
     # Summary files will have an absolute path that will make the index
-    # impossible to use in other processes- we can fix that
+    # impossible to use in other processes - fix paths and rename atomically
     if [ -d bbsplit_build/ref/genome ]; then
-        for summary_file in \$(find bbsplit_build/ref/genome -name summary.txt); do
-            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit_build|bbsplit_index|')
-            sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+        find bbsplit_build/ref/genome -name summary.txt | while read -r summary_file; do
+            sed "s|^source.*|source\\t\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit_build|bbsplit_index|')|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
         done
-
-        # Atomically rename the completed index
         mv bbsplit_build bbsplit_index
     fi