diff --git a/core/src/main/java/io/substrait/relation/ProtoRelConverter.java b/core/src/main/java/io/substrait/relation/ProtoRelConverter.java
index b8a28f78c..ea68adf70 100644
--- a/core/src/main/java/io/substrait/relation/ProtoRelConverter.java
+++ b/core/src/main/java/io/substrait/relation/ProtoRelConverter.java
@@ -719,33 +719,20 @@ protected Aggregate newAggregate(AggregateRel rel) {
 
     List<Aggregate.Grouping> groupings = new ArrayList<>(rel.getGroupingsCount());
 
-    // Groupings are set using the AggregateRel grouping_expression mechanism
-    if (!rel.getGroupingExpressionsList().isEmpty()) {
-      List<Expression> allGroupingExpressions =
-          rel.getGroupingExpressionsList().stream()
-              .map(protoExprConverter::from)
-              .collect(java.util.stream.Collectors.toList());
-
-      for (AggregateRel.Grouping grouping : rel.getGroupingsList()) {
-        List<Integer> references = grouping.getExpressionReferencesList();
-        List<Expression> groupExpressions = new ArrayList<>();
-        for (int ref : references) {
-          groupExpressions.add(allGroupingExpressions.get(ref));
-        }
-        groupings.add(Aggregate.Grouping.builder().addAllExpressions(groupExpressions).build());
-      }
+    // Convert grouping expressions from the aggregate-level grouping_expressions list
+    // Each grouping references expressions by index into this list
+    List<Expression> allGroupingExpressions =
+        rel.getGroupingExpressionsList().stream()
+            .map(protoExprConverter::from)
+            .collect(java.util.stream.Collectors.toList());
 
-    } else {
-      // Groupings are set using the deprecated Grouping grouping_expressions mechanism
-      for (AggregateRel.Grouping grouping : rel.getGroupingsList()) {
-        groupings.add(
-            Aggregate.Grouping.builder()
-                .expressions(
-                    grouping.getGroupingExpressionsList().stream()
-                        .map(protoExprConverter::from)
-                        .collect(java.util.stream.Collectors.toList()))
-                .build());
+    for (AggregateRel.Grouping grouping : rel.getGroupingsList()) {
+      List<Integer> references = grouping.getExpressionReferencesList();
+      List<Expression> groupExpressions = new ArrayList<>();
+      for (int ref : references) {
+        groupExpressions.add(allGroupingExpressions.get(ref));
       }
+      groupings.add(Aggregate.Grouping.builder().addAllExpressions(groupExpressions).build());
     }
 
     List<Aggregate.Measure> measures = new ArrayList<>(rel.getMeasuresCount());
diff --git a/core/src/main/java/io/substrait/relation/RelProtoConverter.java b/core/src/main/java/io/substrait/relation/RelProtoConverter.java
index 0b9aebada..aa92ee9ea 100644
--- a/core/src/main/java/io/substrait/relation/RelProtoConverter.java
+++ b/core/src/main/java/io/substrait/relation/RelProtoConverter.java
@@ -216,8 +216,6 @@ private AggregateRel.Measure toProto(Aggregate.Measure measure) {
   private AggregateRel.Grouping toProto(
       Aggregate.Grouping grouping, List<Expression> uniqueGroupingExpressions) {
     return AggregateRel.Grouping.newBuilder()
-        .addAllGroupingExpressions(
-            grouping.getExpressions().stream().map(this::toProto).collect(Collectors.toList()))
         .addAllExpressionReferences(
             grouping.getExpressions().stream()
                 .map(e -> uniqueGroupingExpressions.indexOf(e))
diff --git a/core/src/test/java/io/substrait/relation/AggregateRelTest.java b/core/src/test/java/io/substrait/relation/AggregateRelTest.java
index 07f1e25cd..25028ca64 100644
--- a/core/src/test/java/io/substrait/relation/AggregateRelTest.java
+++ b/core/src/test/java/io/substrait/relation/AggregateRelTest.java
@@ -73,27 +73,15 @@ private static List<List<Integer>> getExpressionReferences(AggregateRel aggregat
         .collect(Collectors.toList());
   }
 
-  /**
-   * Helper method to extract deprecated grouping expressions from an AggregateRel.
-   *
-   * @param aggregateRel the AggregateRel to extract grouping expressions from
-   * @return a list of lists, where each inner list contains the grouping expressions for a grouping
-   */
-  private static List<List<Expression>> getGroupingExpressions(AggregateRel aggregateRel) {
-    return aggregateRel.getGroupingsList().stream()
-        .map(grouping -> grouping.getGroupingExpressionsList())
-        .collect(Collectors.toList());
-  }
-
   @Test
-  void testDeprecatedGroupingExpressionConversion() {
+  void testGroupingExpressionConversion() {
     Expression col1Ref = createFieldReference(0);
     Expression col2Ref = createFieldReference(1);
 
     AggregateRel.Grouping grouping =
         AggregateRel.Grouping.newBuilder()
-            .addGroupingExpressions(col1Ref) // deprecated proto form
-            .addGroupingExpressions(col2Ref)
+            .addExpressionReferences(0)
+            .addExpressionReferences(1)
             .build();
 
     // Build an input ReadRel
@@ -103,10 +91,12 @@ void testDeprecatedGroupingExpressionConversion() {
             .setBaseSchema(namedStruct)
             .build();
 
-    // Build the AggregateRel with the new grouping_expressions field
+    // Build the AggregateRel with grouping_expressions field
     AggregateRel aggrProto =
         AggregateRel.newBuilder()
             .setInput(Rel.newBuilder().setRead(readProto))
+            .addGroupingExpressions(col1Ref)
+            .addGroupingExpressions(col2Ref)
             .addGroupings(grouping)
             .build();
 
@@ -123,10 +113,8 @@ void testDeprecatedGroupingExpressionConversion() {
     assertTrue(roundtripRel.hasAggregate());
 
     AggregateRel roundtripAgg = roundtripRel.getAggregate();
-    // Verify new expression_references structure
+    // Verify expression_references structure
     assertEquals(List.of(List.of(0, 1)), getExpressionReferences(roundtripAgg));
-    // Verify backward compatibility: deprecated grouping_expressions field is also populated
-    assertEquals(List.of(List.of(col1Ref, col2Ref)), getGroupingExpressions(roundtripAgg));
     // Verify aggregate-level grouping_expressions field is populated
     assertEquals(List.of(col1Ref, col2Ref), roundtripAgg.getGroupingExpressionsList());
   }
@@ -149,7 +137,7 @@ void testAggregateWithSingleGrouping() {
             .setBaseSchema(namedStruct)
             .build();
 
-    // Build the AggregateRel with the new grouping_expressions field
+    // Build the AggregateRel with grouping_expressions field
     AggregateRel aggrProto =
         AggregateRel.newBuilder()
             .setInput(Rel.newBuilder().setRead(readProto))
@@ -171,10 +159,8 @@ void testAggregateWithSingleGrouping() {
     assertTrue(roundtripRel.hasAggregate());
 
     AggregateRel roundtripAgg = roundtripRel.getAggregate();
-    // Verify new expression_references structure
+    // Verify expression_references structure
     assertEquals(List.of(List.of(0, 1)), getExpressionReferences(roundtripAgg));
-    // Verify backward compatibility: deprecated grouping_expressions field is also populated
-    assertEquals(List.of(List.of(col1Ref, col2Ref)), getGroupingExpressions(roundtripAgg));
     // Verify aggregate-level grouping_expressions field is populated
     assertEquals(List.of(col1Ref, col2Ref), roundtripAgg.getGroupingExpressionsList());
   }
@@ -200,7 +186,7 @@ void testAggregateWithMultipleGroupings() {
             .setBaseSchema(namedStruct)
             .build();
 
-    // Build the AggregateRel with the new grouping_expressions field
+    // Build the AggregateRel with grouping_expressions field
     AggregateRel aggrProto =
         AggregateRel.newBuilder()
             .setInput(Rel.newBuilder().setRead(readProto))
@@ -224,11 +210,8 @@ void testAggregateWithMultipleGroupings() {
     assertTrue(roundtripRel.hasAggregate());
 
     AggregateRel roundtripAgg = roundtripRel.getAggregate();
-    // Verify new expression_references structure
+    // Verify expression_references structure
     assertEquals(List.of(List.of(0, 1), List.of(1)), getExpressionReferences(roundtripAgg));
-    // Verify backward compatibility: deprecated grouping_expressions field is also populated
-    assertEquals(
-        List.of(List.of(col1Ref, col2Ref), List.of(col2Ref)), getGroupingExpressions(roundtripAgg));
     // Verify aggregate-level grouping_expressions field is populated
     assertEquals(List.of(col1Ref, col2Ref), roundtripAgg.getGroupingExpressionsList());
   }