diff --git a/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java b/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java
index 0aef61857..b39fce72a 100644
--- a/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java
+++ b/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java
@@ -285,10 +285,6 @@ public RelNode visit(Set set, Context context) throws RuntimeException {
             input -> {
               relBuilder.push(input.accept(this, context));
             });
-    // TODO: MINUS_MULTISET and INTERSECTION_PRIMARY mappings are set to be removed as they do not
-    //   correspond to the Calcite relations they are associated with. They are retained for now
-    //   to enable users to migrate off of them.
-    //   See:  https://github.com/substrait-io/substrait-java/issues/303
     RelBuilder builder = getRelBuilder(set);
     RelNode node = builder.build();
     return applyRemap(node, set.getRemap());
@@ -301,9 +297,7 @@ private RelBuilder getRelBuilder(Set set) {
       case MINUS_PRIMARY:
         return relBuilder.minus(false, numInputs);
       case MINUS_PRIMARY_ALL:
-      case MINUS_MULTISET:
         return relBuilder.minus(true, numInputs);
-      case INTERSECTION_PRIMARY:
       case INTERSECTION_MULTISET:
         return relBuilder.intersect(false, numInputs);
       case INTERSECTION_MULTISET_ALL:
diff --git a/isthmus/src/test/java/io/substrait/isthmus/SubstraitRelNodeConverterTest.java b/isthmus/src/test/java/io/substrait/isthmus/SubstraitRelNodeConverterTest.java
index 7ac6f9f66..4a5ed1f9e 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/SubstraitRelNodeConverterTest.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/SubstraitRelNodeConverterTest.java
@@ -1,5 +1,7 @@
 package io.substrait.isthmus;
 
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
 import io.substrait.plan.Plan;
 import io.substrait.relation.Join.JoinType;
 import io.substrait.relation.Rel;
@@ -242,6 +244,24 @@ void emit() {
       RelNode relNode = substraitToCalcite.convert(root.getInput());
       assertRowMatch(relNode.getRowType(), R.I32, N.STRING);
     }
+
+    // MINUS_MULTISET and INTERSECTION_PRIMARY have no equivalent Calcite relation, so converting
+    // them to Calcite is unsupported.
+    @Test
+    void minusMultisetUnsupported() {
+      Plan.Root root = sb.root(sb.set(SetOp.MINUS_MULTISET, commonTable, commonTable));
+
+      assertThrows(
+          UnsupportedOperationException.class, () -> substraitToCalcite.convert(root.getInput()));
+    }
+
+    @Test
+    void intersectionPrimaryUnsupported() {
+      Plan.Root root = sb.root(sb.set(SetOp.INTERSECTION_PRIMARY, commonTable, commonTable));
+
+      assertThrows(
+          UnsupportedOperationException.class, () -> substraitToCalcite.convert(root.getInput()));
+    }
   }
 
   @Nested
diff --git a/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java b/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java
index 3e57905e2..5d8b5a089 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java
@@ -59,7 +59,8 @@ private static String asString(Set.SetOp op) {
   }
 
   // Generate all SetOp types excluding:
-  // * MINUS_MULTISET, INTERSECTION_PRIMARY: do not map to Calcite relations
+  // * MINUS_MULTISET, INTERSECTION_PRIMARY: no equivalent Calcite relation, so they are
+  //   unsupported in Substrait -> Calcite conversion
   // * UNKNOWN: invalid
   public static Stream<Arguments> setTestConfig() {
     return Arrays.stream(Set.SetOp.values())