diff --git a/gtsam/hybrid/HybridBayesTree.cpp b/gtsam/hybrid/HybridBayesTree.cpp
index 193635a21..1b633e024 100644
--- a/gtsam/hybrid/HybridBayesTree.cpp
+++ b/gtsam/hybrid/HybridBayesTree.cpp
@@ -210,9 +210,11 @@ void HybridBayesTree::prune(const size_t maxNrLeaves) {
       if (conditional->isHybrid()) {
         auto hybridGaussianCond = conditional->asHybrid();
 
-        // Imperative
-        clique->conditional() = std::make_shared<HybridConditional>(
-            hybridGaussianCond->prune(parentData.prunedDiscreteProbs));
+        if (!hybridGaussianCond->pruned()) {
+          // Imperative
+          clique->conditional() = std::make_shared<HybridConditional>(
+              hybridGaussianCond->prune(parentData.prunedDiscreteProbs));
+        }
       }
       return parentData;
     }
diff --git a/gtsam/hybrid/HybridGaussianConditional.cpp b/gtsam/hybrid/HybridGaussianConditional.cpp
index 1bec42810..54346679e 100644
--- a/gtsam/hybrid/HybridGaussianConditional.cpp
+++ b/gtsam/hybrid/HybridGaussianConditional.cpp
@@ -120,7 +120,7 @@ struct HybridGaussianConditional::Helper {
 
 /* *******************************************************************************/
 HybridGaussianConditional::HybridGaussianConditional(
-    const DiscreteKeys &discreteParents, Helper &&helper)
+    const DiscreteKeys &discreteParents, Helper &&helper, bool pruned)
     : BaseFactor(discreteParents,
                  FactorValuePairs(
                      [&](const GaussianFactorValuePair
@@ -130,7 +130,8 @@ HybridGaussianConditional::HybridGaussianConditional(
                      },
                      std::move(helper.pairs))),
       BaseConditional(*helper.nrFrontals),
-      negLogConstant_(helper.minNegLogConstant) {}
+      negLogConstant_(helper.minNegLogConstant),
+      pruned_(pruned) {}
 
 HybridGaussianConditional::HybridGaussianConditional(
     const DiscreteKey &discreteParent,
@@ -166,8 +167,9 @@ HybridGaussianConditional::HybridGaussianConditional(
     : HybridGaussianConditional(discreteParents, Helper(conditionals)) {}
 
 HybridGaussianConditional::HybridGaussianConditional(
-    const DiscreteKeys &discreteParents, const FactorValuePairs &pairs)
-    : HybridGaussianConditional(discreteParents, Helper(pairs)) {}
+    const DiscreteKeys &discreteParents, const FactorValuePairs &pairs,
+    bool pruned)
+    : HybridGaussianConditional(discreteParents, Helper(pairs), pruned) {}
 
 /* *******************************************************************************/
 const HybridGaussianConditional::Conditionals
@@ -331,7 +333,7 @@ HybridGaussianConditional::shared_ptr HybridGaussianConditional::prune(
 
   FactorValuePairs prunedConditionals = factors().apply(pruner);
   return std::make_shared<HybridGaussianConditional>(discreteKeys(),
-                                                     prunedConditionals);
+                                                     prunedConditionals, true);
 }
 
 /* *******************************************************************************/
diff --git a/gtsam/hybrid/HybridGaussianConditional.h b/gtsam/hybrid/HybridGaussianConditional.h
index c485fafce..0d2b1323c 100644
--- a/gtsam/hybrid/HybridGaussianConditional.h
+++ b/gtsam/hybrid/HybridGaussianConditional.h
@@ -68,6 +68,9 @@ class GTSAM_EXPORT HybridGaussianConditional
   ///< Take advantage of the neg-log space so everything is a minimization
   double negLogConstant_;
 
+  /// Flag to indicate if the conditional has been pruned.
+  bool pruned_ = false;
+
  public:
   /// @name Constructors
   /// @{
@@ -150,9 +153,10 @@ class GTSAM_EXPORT HybridGaussianConditional
    *
    * @param discreteParents the discrete parents. Will be placed last.
    * @param conditionalPairs Decision tree of GaussianFactor/scalar pairs.
+   * @param pruned Flag indicating if conditional has been pruned.
    */
   HybridGaussianConditional(const DiscreteKeys &discreteParents,
-                            const FactorValuePairs &pairs);
+                            const FactorValuePairs &pairs, bool pruned = false);
 
   /// @}
   /// @name Testable
@@ -233,6 +237,9 @@ class GTSAM_EXPORT HybridGaussianConditional
   HybridGaussianConditional::shared_ptr prune(
       const DecisionTreeFactor &discreteProbs) const;
 
+  /// Return true if the conditional has already been pruned.
+  bool pruned() const { return pruned_; }
+
   /// @}
 
  private:
@@ -241,7 +248,7 @@ class GTSAM_EXPORT HybridGaussianConditional
 
   /// Private constructor that uses helper struct above.
   HybridGaussianConditional(const DiscreteKeys &discreteParents,
-                            Helper &&helper);
+                            Helper &&helper, bool pruned = false);
 
   /// Check whether `given` has values for all frontal keys.
   bool allFrontalsGiven(const VectorValues &given) const;