diff --git a/src/PKSim.Core/Mappers/ProcessToProcessBuilderMapper.cs b/src/PKSim.Core/Mappers/ProcessToProcessBuilderMapper.cs
index 4fad1e9fb..38ffcb9ba 100644
--- a/src/PKSim.Core/Mappers/ProcessToProcessBuilderMapper.cs
+++ b/src/PKSim.Core/Mappers/ProcessToProcessBuilderMapper.cs
@@ -12,6 +12,7 @@
 using PKSim.Core.Repositories;
 using PKSim.Core.Services;
 using static PKSim.Core.CoreConstants.Compartment;
+using static PKSim.Core.CoreConstants.Organ;
 
 namespace PKSim.Core.Mappers
 {
@@ -187,7 +188,7 @@ public IReactionBuilder InductionReactionFrom(InteractionProcess interactionProc
          reaction.AddProduct(new ReactionPartnerBuilder(protein.Name, 1));
 
          //Induction occurs only in Intracellular and Interstitial
-         reaction.ContainerCriteria.Add(new InContainerCondition(CoreConstants.Organ.TISSUE_ORGAN));
+         reaction.ContainerCriteria.Add(new InContainerCondition(TISSUE_ORGAN));
          reaction.ContainerCriteria.Add(new NotMatchTagCondition(PLASMA));
          reaction.ContainerCriteria.Add(new NotMatchTagCondition(BLOOD_CELLS));
          reaction.ContainerCriteria.Add(new NotMatchTagCondition(ENDOSOME));
@@ -359,8 +360,9 @@ private IReadOnlyCollection<InducedProcess> allInducedProcessesFor(IndividualTra
                   inducedProcessCache.Add(inducedProcess);
                }
 
-               inducedProcess.AddSourceOrgan(transportTemplate.SourceOrgan);
-               inducedProcess.AddTargetOrgan(transportTemplate.TargetOrgan);
+               // For lumen transport. The source organ or target organ is in fact defined as a compartment
+               inducedProcess.AddSourceOrgan(transportTemplate.SourceOrgan.IsLumen() ? transportTemplate.SourceCompartment : transportTemplate.SourceOrgan);
+               inducedProcess.AddTargetOrgan(transportTemplate.TargetOrgan.IsLumen() ? transportTemplate.TargetCompartment : transportTemplate.TargetOrgan);
             }
          }
 
@@ -369,19 +371,36 @@ private IReadOnlyCollection<InducedProcess> allInducedProcessesFor(IndividualTra
 
       private void updateTransporterTagsFor(ITransportBuilder transporterBuilder, InducedProcess inducedProcess)
       {
-         var allSourceTags = transporterBuilder.SourceCriteria.OfType<TagCondition>()
-            .Select(x => x.Tag).ToList();
+         var sourceCriteria = transporterBuilder.SourceCriteria;
+         var allSourceTags = sourceCriteria.OfType<MatchTagCondition>().Select(x => x.Tag).ToList();
+         var (sourceIsLumen, sourceIsMucosa) = (allSourceTags.Contains(LUMEN), allSourceTags.Contains(MUCOSA));
 
-         //More than one tag coming from the database => This is a specific transport and we do not need to do anything
-         if (allSourceTags.Count > 1)
-            return;
+         var targetCriteria = transporterBuilder.TargetCriteria;
+         var allTargetTags = targetCriteria.OfType<MatchTagCondition>().Select(x => x.Tag).ToList();
+         var (targetIsLumen, targetIsMucosa) = (allTargetTags.Contains(LUMEN), allTargetTags.Contains(MUCOSA));
+
+         var isLumen = sourceIsLumen || targetIsLumen;
+         var isMucosa = sourceIsMucosa || targetIsMucosa;
 
-         foreach (var organName in inducedProcess.OrgansToExclude)
+         if (isLumen && isMucosa)
          {
-            transporterBuilder.SourceCriteria.Add(new NotMatchTagCondition(organName));
+            //We just want to remove GI segments from the include list as we know, that the transport is between Lumen and Mucosa in this case
+            var segmentToDeletes = inducedProcess.OrgansToExclude.Intersect(LumenSegmentsDuodenumToRectum).ToList();
+            var criteria = sourceIsLumen ? sourceCriteria : targetCriteria;
+            addAsNotMatchToCriteria(criteria, segmentToDeletes);
+            return;
          }
+
+         // This is a specific transport and we do not need to do anything
+         if (allSourceTags.Count > 1)
+            return;
+
+         addAsNotMatchToCriteria(sourceCriteria, inducedProcess.OrgansToExclude);
       }
 
+      private void addAsNotMatchToCriteria(DescriptorCriteria criteria, IEnumerable<string> list)
+         => list.Each(x => criteria.Add(new NotMatchTagCondition(x)));
+
       private ITransportBuilder activeTransportFrom(CompoundProcess process, InducedProcess inducedProcess, IFormulaCache formulaCache)
       {
          //retrieve process for the simulation and create a clone
diff --git a/tests/PKSim.Tests/Data/Mucosa_MultipleTransportDirections.pksim5 b/tests/PKSim.Tests/Data/Mucosa_MultipleTransportDirections.pksim5
new file mode 100644
index 000000000..d84d1a14e
Binary files /dev/null and b/tests/PKSim.Tests/Data/Mucosa_MultipleTransportDirections.pksim5 differ
diff --git a/tests/PKSim.Tests/IntegrationTests/ProcessToProcessBuilderMapperSpecs.cs b/tests/PKSim.Tests/IntegrationTests/ProcessToProcessBuilderMapperSpecs.cs
new file mode 100644
index 000000000..fa8308bff
--- /dev/null
+++ b/tests/PKSim.Tests/IntegrationTests/ProcessToProcessBuilderMapperSpecs.cs
@@ -0,0 +1,40 @@
+using System.Linq;
+using OSPSuite.BDDHelper;
+using OSPSuite.BDDHelper.Extensions;
+using OSPSuite.Core.Domain;
+using PKSim.Core.Mappers;
+using PKSim.Core.Model;
+using PKSim.Infrastructure;
+
+namespace PKSim.IntegrationTests
+{
+   public abstract class concern_for_ProcessToProcessBuilderMapper : ContextWithLoadedProject<IProcessToProcessBuilderMapper>
+   {
+      public override void GlobalContext()
+      {
+         base.GlobalContext();
+         LoadProject("Mucosa_MultipleTransportDirections");
+      }
+   }
+
+   public class When_creating_a_simulation_using_transport_in_multiple_mucosa_directions : concern_for_ProcessToProcessBuilderMapper
+   {
+      private Simulation _simulation;
+
+      protected override void Context()
+      {
+         base.Context();
+         var ind = FindByName<Individual>("I1");
+         var comp = FindByName<Compound>("C1");
+         var prot = FindByName<Protocol>("IV");
+         _simulation = DomainFactoryForSpecs.CreateSimulationWith(ind, comp, prot);
+      }
+
+      [Observation]
+      public void should_not_create_too_many_transporters()
+      {
+         var transportInLumenToMucosa = _simulation.Model.Neighborhoods.EntityAt<IContainer>("Lumen_lil_LowerIleum_cell", "C1", "T1-a");
+         transportInLumenToMucosa.GetChildren<IContainer>(x => x.ContainerType == ContainerType.Transport).Count().ShouldBeEqualTo(1);
+      }
+   }
+}
\ No newline at end of file