diff --git a/Detectors/Base/include/DetectorsBase/Aligner.h b/Detectors/Base/include/DetectorsBase/Aligner.h
index 0b378dcfa33cb..12eb7dfee003c 100644
--- a/Detectors/Base/include/DetectorsBase/Aligner.h
+++ b/Detectors/Base/include/DetectorsBase/Aligner.h
@@ -33,7 +33,7 @@ class Aligner : public o2::conf::ConfigurableParamHelper<Aligner>
   o2::detectors::DetID::mask_t getDetectorsMask() const;
 
   bool isAlignmentRequested() const { return getDetectorsMask().any(); }
-  void applyAlignment(long timestamp = 0, o2::detectors::DetID::mask_t addMask = o2::detectors::DetID::FullMask) const;
+  void applyAlignment(long timestamp = 0, o2::detectors::DetID::mask_t addMask = o2::detectors::DetID::FullMask, bool keepPhysicalNodes = true) const;
 
  private:
   std::string mDetectors = "all";                      // comma-separated list of modules to align, "all" or "none"
diff --git a/Detectors/Base/include/DetectorsBase/GeometryManager.h b/Detectors/Base/include/DetectorsBase/GeometryManager.h
index f918c278dcf33..6c771aa4bc936 100644
--- a/Detectors/Base/include/DetectorsBase/GeometryManager.h
+++ b/Detectors/Base/include/DetectorsBase/GeometryManager.h
@@ -84,7 +84,8 @@ class GeometryManager : public TObject
   ~GeometryManager() override = default;
 
   /// misalign geometry with alignment objects from the array, optionaly check overlaps
-  static bool applyAlignment(const std::vector<o2::detectors::AlignParam>& algPars);
+  /// with keepPhysicalNodes false, each physical node is deleted after its alignment (no original matrices are kept)
+  static bool applyAlignment(const std::vector<o2::detectors::AlignParam>& algPars, bool keepPhysicalNodes = true);
   static bool applyAlignment(const std::vector<const std::vector<o2::detectors::AlignParam>*> algPars);
 
   struct MatBudgetExt {
diff --git a/Detectors/Base/src/Aligner.cxx b/Detectors/Base/src/Aligner.cxx
index a82f48942d2be..70f5f9f96a453 100644
--- a/Detectors/Base/src/Aligner.cxx
+++ b/Detectors/Base/src/Aligner.cxx
@@ -27,7 +27,7 @@ DetID::mask_t Aligner::getDetectorsMask() const
   return DetID::getMask(mDetectors) & (~DetID::getMask(DetID::CTP));
 }
 
-void Aligner::applyAlignment(long timestamp, DetID::mask_t addMask) const
+void Aligner::applyAlignment(long timestamp, DetID::mask_t addMask, bool keepPhysicalNodes) const
 {
   DetID::mask_t msk = getDetectorsMask() & addMask;
   if (msk.none()) {
@@ -59,7 +59,7 @@ void Aligner::applyAlignment(long timestamp, DetID::mask_t addMask) const
     }
     if (!algV->empty()) {
       done.set(id);
-      o2::base::GeometryManager::applyAlignment(*algV);
+      o2::base::GeometryManager::applyAlignment(*algV, keepPhysicalNodes);
     } else {
       skipped.set(id);
     }
diff --git a/Detectors/Base/src/GeometryManager.cxx b/Detectors/Base/src/GeometryManager.cxx
index f0ea0d41e7d04..ecc279dab1db2 100644
--- a/Detectors/Base/src/GeometryManager.cxx
+++ b/Detectors/Base/src/GeometryManager.cxx
@@ -277,7 +277,7 @@ bool GeometryManager::applyAlignment(const std::vector<const std::vector<o2::det
 }
 
 //______________________________________________________________________
-bool GeometryManager::applyAlignment(const std::vector<o2::detectors::AlignParam>& algPars)
+bool GeometryManager::applyAlignment(const std::vector<o2::detectors::AlignParam>& algPars, bool keepPhysicalNodes)
 {
   /// misalign geometry with alignment objects from the array, optionaly check overlaps
   int nvols = algPars.size();
@@ -286,11 +286,23 @@ bool GeometryManager::applyAlignment(const std::vector<o2::detectors::AlignParam
   std::sort(std::begin(ord), std::end(ord), [&algPars](int a, int b) { return algPars[a].getLevel() < algPars[b].getLevel(); });
 
   bool res = true;
+  auto pns = gGeoManager->GetListOfPhysicalNodes();
   for (int i = 0; i < nvols; i++) {
+    int npn = pns->GetEntriesFast();
     if (!algPars[ord[i]].applyToGeometry(GeometryManagerParam::Instance().printLevel)) {
       res = false;
       LOG(error) << "Error applying alignment object for volume" << algPars[ord[i]].getSymName();
     }
+    if (!keepPhysicalNodes) { // delete the nodes this alignment created, so their memory is reused by the next one
+      for (int k = pns->GetEntriesFast() - 1; k >= npn; k--) {
+        auto pn = static_cast<TGeoPhysicalNode*>(pns->RemoveAt(k));
+        if (auto pne = gGeoManager->GetAlignableEntry(algPars[ord[i]].getSymName().c_str()); pne && pne->GetPhysicalNode() == pn) {
+          pne->SetPhysicalNode(nullptr);
+        }
+        delete pn;
+      }
+      pns->Compress();
+    }
   }
   return res;
 }
diff --git a/Steer/src/O2MCApplication.cxx b/Steer/src/O2MCApplication.cxx
index b3bbe0e59223e..e79264744d3ac 100644
--- a/Steer/src/O2MCApplication.cxx
+++ b/Steer/src/O2MCApplication.cxx
@@ -330,7 +330,8 @@ bool O2MCApplicationBase::MisalignGeometry()
 
   // apply alignment for included detectors AFTER exporting ideal geometry
   auto& aligner = o2::base::Aligner::Instance();
-  aligner.applyAlignment(confref.getTimestamp());
+  // the simulation needs no original matrices, so the physical nodes are not kept
+  aligner.applyAlignment(confref.getTimestamp(), o2::detectors::DetID::FullMask, false);
 
   // export aligned geometry into different file
   auto alignedgeomfile = o2::base::NameConf::getAlignedGeomFileName(confref.getOutPrefix());