diff --git a/Framework/Core/include/Framework/CommonLabels.h b/Framework/Core/include/Framework/CommonLabels.h
index 8be41a33af41d..17b1c85bf6fe4 100644
--- a/Framework/Core/include/Framework/CommonLabels.h
+++ b/Framework/Core/include/Framework/CommonLabels.h
@@ -21,6 +21,11 @@ namespace o2::framework
 // When present on a DataProcessor, no DomainInfoHeader messages will be sent downstream.
 const extern DataProcessorLabel suppressDomainInfoLabel;
 
+// Label to allow multiple DataProcessorSpecs with the same name in the topology.
+// When present, duplicate specs with matching inputs and outputs will be deduplicated
+// with a warning instead of causing a fatal error.
+const extern DataProcessorLabel allowDuplicatesLabel;
+
 } // namespace o2::framework
 
 #endif // O2_FRAMEWORK_COMMONLABELS_H
diff --git a/Framework/Core/src/CommonLabels.cxx b/Framework/Core/src/CommonLabels.cxx
index f728e194f611b..d660bdd84c6db 100644
--- a/Framework/Core/src/CommonLabels.cxx
+++ b/Framework/Core/src/CommonLabels.cxx
@@ -15,5 +15,6 @@ namespace o2::framework
 {
 
 const DataProcessorLabel suppressDomainInfoLabel = {"suppress-domain-info"};
+const DataProcessorLabel allowDuplicatesLabel = {"allow-duplicates"};
 
 } // namespace o2::framework
diff --git a/Framework/Core/src/WorkflowHelpers.cxx b/Framework/Core/src/WorkflowHelpers.cxx
index 188b6653c6a43..6d3630d6c0aa8 100644
--- a/Framework/Core/src/WorkflowHelpers.cxx
+++ b/Framework/Core/src/WorkflowHelpers.cxx
@@ -11,10 +11,12 @@
 #include "WorkflowHelpers.h"
 #include "Framework/AnalysisSupportHelpers.h"
 #include "Framework/AlgorithmSpec.h"
+#include "Framework/CommonLabels.h"
 #include "Framework/ConfigParamSpec.h"
 #include "Framework/ConfigParamsHelper.h"
 #include "Framework/CommonDataProcessors.h"
 #include "Framework/ConfigContext.h"
+#include "Framework/DataProcessorSpecHelpers.h"
 #include "Framework/DeviceSpec.h"
 #include "Framework/DataSpecUtils.h"
 #include "Framework/DataSpecViews.h"
@@ -32,6 +34,7 @@
 #include "Headers/DataHeader.h"
 #include <algorithm>
 #include <list>
+#include <map>
 #include <set>
 #include <utility>
 #include <vector>
@@ -959,7 +962,7 @@ WorkflowParsingState WorkflowHelpers::verifyWorkflow(const o2::framework::Workfl
   if (workflow.empty()) {
     return WorkflowParsingState::Empty;
   }
-  std::set<std::string> validNames;
+  std::map<std::string, size_t> validNames;
   // std::vector<OutputSpec> availableOutputs;
   // std::vector<InputSpec> requiredInputs;
 
@@ -971,17 +974,25 @@ WorkflowParsingState WorkflowHelpers::verifyWorkflow(const o2::framework::Workfl
 
   std::ostringstream ss;
 
-  for (auto& spec : workflow) {
+  for (size_t si = 0; si < workflow.size(); ++si) {
+    auto& spec = workflow[si];
     if (spec.name.empty()) {
       throw std::runtime_error("Invalid DataProcessorSpec name");
     }
     if (strpbrk(spec.name.data(), ",;:\"'$") != nullptr) {
       throw std::runtime_error("Cannot use any of ,;:\"'$ as DataProcessor name");
     }
-    if (validNames.find(spec.name) != validNames.end()) {
-      throw std::runtime_error("Name " + spec.name + " is used twice.");
+    auto it = validNames.find(spec.name);
+    if (it != validNames.end()) {
+      auto& firstSpec = workflow[it->second];
+      if (!DataProcessorSpecHelpers::hasLabel(firstSpec, allowDuplicatesLabel.value.c_str()) ||
+          !DataProcessorSpecHelpers::hasLabel(spec, allowDuplicatesLabel.value.c_str())) {
+        throw std::runtime_error("Name " + spec.name + " is used twice.");
+      }
+      LOG(warning) << "Duplicate DataProcessorSpec " << spec.name << " found with allow-duplicates label. Will be deduplicated.";
+      continue;
     }
-    validNames.insert(spec.name);
+    validNames.emplace(spec.name, si);
     for (auto& option : spec.options) {
       if (option.defaultValue.type() != VariantType::Empty &&
           option.type != option.defaultValue.type()) {
@@ -1005,6 +1016,22 @@ WorkflowParsingState WorkflowHelpers::verifyWorkflow(const o2::framework::Workfl
   return WorkflowParsingState::Valid;
 }
 
+void WorkflowHelpers::removeDuplicates(WorkflowSpec& workflow)
+{
+  std::set<std::string> seen;
+  auto it = std::remove_if(workflow.begin(), workflow.end(), [&seen](DataProcessorSpec const& spec) {
+    if (seen.find(spec.name) == seen.end()) {
+      seen.insert(spec.name);
+      return false;
+    }
+    if (!DataProcessorSpecHelpers::hasLabel(spec, allowDuplicatesLabel.value.c_str())) {
+      return false;
+    }
+    return true;
+  });
+  workflow.erase(it, workflow.end());
+}
+
 using UnifiedDataSpecType = std::variant<InputSpec, OutputSpec>;
 struct DataMatcherId {
   size_t workflowId;
diff --git a/Framework/Core/src/WorkflowHelpers.h b/Framework/Core/src/WorkflowHelpers.h
index 5c0aa363c6d67..c7a990cd2730c 100644
--- a/Framework/Core/src/WorkflowHelpers.h
+++ b/Framework/Core/src/WorkflowHelpers.h
@@ -175,6 +175,10 @@ struct WorkflowHelpers {
   // it contains no empty labels.
   [[nodiscard]] static WorkflowParsingState verifyWorkflow(const WorkflowSpec& workflow);
 
+  // Remove duplicate DataProcessorSpecs that have the "allow-duplicates" label.
+  // Duplicate specs must have the same inputs and outputs, otherwise an exception is thrown.
+  static void removeDuplicates(WorkflowSpec& workflow);
+
   // Depending on the workflow and the dangling inputs inside it, inject "fake"
   // devices to mark the fact we might need some extra action to make sure
   // dangling inputs are satisfied.
diff --git a/Framework/Core/src/runDataProcessing.cxx b/Framework/Core/src/runDataProcessing.cxx
index c58f8e7287b3b..17be198db8a5e 100644
--- a/Framework/Core/src/runDataProcessing.cxx
+++ b/Framework/Core/src/runDataProcessing.cxx
@@ -1663,6 +1663,7 @@ int runStateMachine(DataProcessorSpecs const& workflow,
           /// extract and apply process switches
           /// prune device inputs
           auto altered_workflow = workflow;
+          WorkflowHelpers::removeDuplicates(altered_workflow);
 
           auto confNameFromParam = [](std::string const& paramName) {
             std::regex name_regex(R"(^control:([\w-]+)\/(\w+))");
diff --git a/Framework/Core/test/test_WorkflowHelpers.cxx b/Framework/Core/test/test_WorkflowHelpers.cxx
index d43e74558c0bb..9e219fc0dfb83 100644
--- a/Framework/Core/test/test_WorkflowHelpers.cxx
+++ b/Framework/Core/test/test_WorkflowHelpers.cxx
@@ -10,6 +10,7 @@
 // or submit itself to any jurisdiction.
 #include "Mocking.h"
 #include "test_HelperMacros.h"
+#include "Framework/CommonLabels.h"
 #include "Framework/ConfigContext.h"
 #include "Framework/WorkflowSpec.h"
 #include "Framework/DataSpecUtils.h"
@@ -60,6 +61,30 @@ TEST_CASE("TestVerifyWorkflow")
   checkOk(WorkflowSpec{{"A", {InputSpec{"x", "TST", "A"}}}});
   // Check for duplicate DataProcessorSpecs names
   checkNotOk(WorkflowSpec{{"A"}, {"A"}});
+  // Duplicates with allow-duplicates label should not throw
+  checkOk(WorkflowSpec{
+    {.name = "A", .labels = {allowDuplicatesLabel}},
+    {.name = "A", .labels = {allowDuplicatesLabel}},
+  });
+  // Duplicates without the label should still throw
+  checkNotOk(WorkflowSpec{
+    {.name = "A"},
+    {.name = "A", .labels = {allowDuplicatesLabel}},
+  });
+}
+
+TEST_CASE("TestRemoveDuplicates")
+{
+  // removeDuplicates should keep only the first spec with a given name
+  WorkflowSpec workflow{
+    {.name = "A", .labels = {allowDuplicatesLabel}},
+    {.name = "B"},
+    {.name = "A", .labels = {allowDuplicatesLabel}},
+  };
+  WorkflowHelpers::removeDuplicates(workflow);
+  REQUIRE(workflow.size() == 2);
+  REQUIRE(workflow[0].name == "A");
+  REQUIRE(workflow[1].name == "B");
 }
 
 TEST_CASE("TestWorkflowHelpers")