diff --git a/include/clad/Differentiator/DerivativeBuilder.h b/include/clad/Differentiator/DerivativeBuilder.h
index 202856c7d..f2981438f 100644
--- a/include/clad/Differentiator/DerivativeBuilder.h
+++ b/include/clad/Differentiator/DerivativeBuilder.h
@@ -83,7 +83,7 @@ namespace clad {
     clang::Sema& m_Sema;
     plugin::CladPlugin& m_CladPlugin;
     clang::ASTContext& m_Context;
-    const DerivedFnCollector& m_DFC;
+    DerivedFnCollector& m_DFC;
     clad::DynamicGraph<DiffRequest>& m_DiffRequestGraph;
     std::unique_ptr<utils::StmtClone> m_NodeCloner;
     clang::NamespaceDecl* m_BuiltinDerivativesNSD;
@@ -135,7 +135,7 @@ namespace clad {
 
   public:
     DerivativeBuilder(clang::Sema& S, plugin::CladPlugin& P,
-                      const DerivedFnCollector& DFC,
+                      DerivedFnCollector& DFC,
                       clad::DynamicGraph<DiffRequest>& DRG);
     ~DerivativeBuilder();
     /// Reset the model use for error estimation (if any).
diff --git a/include/clad/Differentiator/DerivedFnCollector.h b/include/clad/Differentiator/DerivedFnCollector.h
index b20160a44..909285e99 100644
--- a/include/clad/Differentiator/DerivedFnCollector.h
+++ b/include/clad/Differentiator/DerivedFnCollector.h
@@ -27,6 +27,9 @@ class DerivedFnCollector {
   /// Adds a derived function to the collection.
   void Add(const DerivedFnInfo& DFI);
 
+  /// Adds a function to derivative set.
+  void AddToDerivativeSet(const clang::FunctionDecl* FD);
+
   /// Finds a `DerivedFnInfo` object in the collection that satisfies the
   /// given differentiation request.
   DerivedFnInfo Find(const DiffRequest& request) const;
diff --git a/lib/Differentiator/DerivativeBuilder.cpp b/lib/Differentiator/DerivativeBuilder.cpp
index 861f1dc60..9fe899e7b 100644
--- a/lib/Differentiator/DerivativeBuilder.cpp
+++ b/lib/Differentiator/DerivativeBuilder.cpp
@@ -37,7 +37,7 @@ using namespace clang;
 namespace clad {
 
 DerivativeBuilder::DerivativeBuilder(clang::Sema& S, plugin::CladPlugin& P,
-                                     const DerivedFnCollector& DFC,
+                                     DerivedFnCollector& DFC,
                                      clad::DynamicGraph<DiffRequest>& G)
     : m_Sema(S), m_CladPlugin(P), m_Context(S.getASTContext()), m_DFC(DFC),
       m_DiffRequestGraph(G),
@@ -253,6 +253,17 @@ static void registerDerivative(FunctionDecl* derivedFD, Sema& semaRef) {
 
       OverloadedFn =
           m_Sema.ActOnCallExpr(S, UnresolvedLookup, Loc, MARargs, Loc).get();
+
+      // Add the custom derivative to the set of derivatives.
+      // This is required in case the definition of the custom derivative
+      // is not found in the current translation unit and is linked in
+      // from another translation unit.
+      // Adding it to the set of derivatives ensures that the custom
+      // derivative is not differentiated again using numerical
+      // differentiation due to unavailable definition.
+      if (auto* CE = dyn_cast<CallExpr>(OverloadedFn))
+        if (auto* FD = CE->getDirectCallee())
+          m_DFC.AddToDerivativeSet(FD);
     }
     return OverloadedFn;
   }
diff --git a/lib/Differentiator/DerivedFnCollector.cpp b/lib/Differentiator/DerivedFnCollector.cpp
index f32883689..71bc22258 100644
--- a/lib/Differentiator/DerivedFnCollector.cpp
+++ b/lib/Differentiator/DerivedFnCollector.cpp
@@ -8,7 +8,11 @@ void DerivedFnCollector::Add(const DerivedFnInfo& DFI) {
          "`DerivedFnCollector::Add` more than once for the same derivative "
          ". Ideally, we shouldn't do either.");
   m_DerivedFnInfoCollection[DFI.OriginalFn()].push_back(DFI);
-  m_DerivativeSet.insert(DFI.DerivedFn());
+  AddToDerivativeSet(DFI.DerivedFn());
+}
+
+void DerivedFnCollector::AddToDerivativeSet(const clang::FunctionDecl* FD) {
+  m_DerivativeSet.insert(FD);
 }
 
 bool DerivedFnCollector::AlreadyExists(const DerivedFnInfo& DFI) const {
diff --git a/tools/ClangPlugin.h b/tools/ClangPlugin.h
index 3ec1f9be6..3ba226f31 100644
--- a/tools/ClangPlugin.h
+++ b/tools/ClangPlugin.h
@@ -170,11 +170,12 @@ class CladTimerGroup {
     bool HandleTopLevelDecl(clang::DeclGroupRef D) override {
       if (D.isSingleDecl())
         if (auto* FD = llvm::dyn_cast<clang::FunctionDecl>(D.getSingleDecl()))
-          if (m_DFC.IsDerivative(FD)) {
-            assert(!m_Multiplexer &&
-                   "Must happen only if we failed to rearrange the consumers");
+          // If we build the derivative in a non-standard (with no Multiplexer)
+          // setup, we exit early to give control to the non-standard setup for
+          // code generation.
+          // FIXME: This should go away if Cling starts using the clang driver.
+          if (!m_Multiplexer && m_DFC.IsDerivative(FD))
             return true;
-          }
 
       HandleTopLevelDeclForClad(D);
       AppendDelayed({CallKind::HandleTopLevelDecl, D});