diff --git a/taca/illumina/Runs.py b/taca/illumina/Runs.py
index 75829f36..07d46098 100644
--- a/taca/illumina/Runs.py
+++ b/taca/illumina/Runs.py
@@ -853,6 +853,11 @@ def _fix_html_reports_for_complex_lanes(
                 ):
                     html_report_laneBarcode_parser.sample_data.remove(entry)
 
+        # Remove the trailing "_SX" postfix from samples names for BCL Convert when it handles SmartSeq3 libraries
+        for entry in html_report_laneBarcode_parser.sample_data:
+            if "_S" in entry["Sample"]:
+                entry["Sample"] = "_".join(entry["Sample"].split("_")[:2])
+
         # Sort sample_data: first by lane then by sample ID
         html_report_laneBarcode_parser.sample_data = sorted(
             html_report_laneBarcode_parser.sample_data,