diff --git a/HLTrigger/Configuration/python/customizeHLTforCMSSW.py b/HLTrigger/Configuration/python/customizeHLTforCMSSW.py
index bf0bc345665ba..573f407305159 100644
--- a/HLTrigger/Configuration/python/customizeHLTforCMSSW.py
+++ b/HLTrigger/Configuration/python/customizeHLTforCMSSW.py
@@ -198,6 +198,38 @@ def customizeHLTfor49436(process):
 
     return process
 
+def customizeHLTfor49936(process):
+    """
+    Update Pixel comparison and monitoring modules to comply with the
+    SoA-based plugin migration introduced in PR #49936.
+
+    Existing HLT menus use legacy plugin types (e.g.
+    SiPixelPhase1CompareRecHits); this customization updates the C++
+    plugin type in place while preserving:
+      - module labels
+      - parameters
+      - path and task scheduling
+    """
+
+    from HLTrigger.Configuration.common import producers_by_type
+
+    type_map = {
+        "SiPixelPhase1CompareRecHits": "SiPixelCompareRecHitsSoA",
+        "SiPixelPhase1CompareTracks": "SiPixelCompareTracksSoA",
+        "SiPixelCompareVertices": "SiPixelCompareVerticesSoA",
+
+        "SiPixelPhase1MonitorRecHitsSoAAlpaka": "SiPixelMonitorRecHitsSoA",
+        "SiPixelPhase1MonitorTrackSoAAlpaka": "SiPixelMonitorTrackSoA",
+        "SiPixelMonitorVertexSoAAlpaka": "SiPixelMonitorVertexSoA",
+    }
+
+    for old_type, new_type in type_map.items():
+        for module in producers_by_type(process, old_type):
+            module._TypedParameterizable__type = new_type
+
+    return process
+
+
 # CMSSW version specific customizations
 def customizeHLTforCMSSW(process, menuType="GRun"):
 
@@ -207,4 +239,6 @@ def customizeHLTforCMSSW(process, menuType="GRun"):
 
     # process = customizeHLTfor49436(process)
 
+    process = customizeHLTfor49936(process)
+
     return process