diff --git a/native/spark-expr/src/bloom_filter/spark_bloom_filter.rs b/native/spark-expr/src/bloom_filter/spark_bloom_filter.rs
index e84257ea67..f5ed086d27 100644
--- a/native/spark-expr/src/bloom_filter/spark_bloom_filter.rs
+++ b/native/spark-expr/src/bloom_filter/spark_bloom_filter.rs
@@ -160,11 +160,27 @@ impl SparkBloomFilter {
     }
 
     pub fn merge_filter(&mut self, other: &[u8]) {
+        // Extract bits data if other is in Spark's full serialization format
+        // We need to compute the expected size and extract data before borrowing self.bits mutably
+        let expected_bits_size = self.bits.byte_size();
+        const SPARK_HEADER_SIZE: usize = 12; // version (4) + num_hash_functions (4) + num_words (4)
+
+        let bits_data = if other.len() == SPARK_HEADER_SIZE + expected_bits_size {
+            // This is Spark's full format, extract bits data (skip header)
+            &other[SPARK_HEADER_SIZE..]
+        } else {
+            // This is already just bits data (Comet format)
+            other
+        };
+
         assert_eq!(
-            other.len(),
-            self.bits.byte_size(),
-            "Cannot merge SparkBloomFilters with different lengths."
+            bits_data.len(),
+            expected_bits_size,
+            "Cannot merge SparkBloomFilters with different lengths. Expected {} bytes, got {} bytes (full buffer size: {} bytes)",
+            expected_bits_size,
+            bits_data.len(),
+            other.len()
         );
-        self.bits.merge_bits(other);
+        self.bits.merge_bits(bits_data);
     }
 }
diff --git a/spark/src/main/scala/org/apache/spark/sql/comet/operators.scala b/spark/src/main/scala/org/apache/spark/sql/comet/operators.scala
index 0a435e5b7a..7860b8380f 100644
--- a/spark/src/main/scala/org/apache/spark/sql/comet/operators.scala
+++ b/spark/src/main/scala/org/apache/spark/sql/comet/operators.scala
@@ -1069,7 +1069,13 @@ trait CometBaseAggregate {
     val multiMode = modes.size > 1
     // For a final mode HashAggregate, we only need to transform the HashAggregate
     // if there is Comet partial aggregation.
-    val sparkFinalMode = modes.contains(Final) && findCometPartialAgg(aggregate.child).isEmpty
+    // Exception: BloomFilterAggregate supports Spark partial / Comet final because
+    // merge_filter() handles Spark's serialization format (12-byte header + bits).
+    val hasBloomFilterAgg = aggregate.aggregateExpressions.exists(expr =>
+      expr.aggregateFunction.getClass.getSimpleName == "BloomFilterAggregate")
+    val sparkFinalMode = modes.contains(Final) &&
+      findCometPartialAgg(aggregate.child).isEmpty &&
+      !hasBloomFilterAgg
 
     if (multiMode || sparkFinalMode) {
       return None
diff --git a/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala b/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala
index 1b2373ad71..b40ce6c2bb 100644
--- a/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala
+++ b/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala
@@ -36,7 +36,8 @@ import org.apache.spark.sql.catalyst.expressions.aggregate.{AggregateMode, Bloom
 import org.apache.spark.sql.comet._
 import org.apache.spark.sql.comet.execution.shuffle.{CometColumnarShuffle, CometShuffleExchangeExec}
 import org.apache.spark.sql.execution.{CollectLimitExec, ProjectExec, SQLExecution, UnionExec}
-import org.apache.spark.sql.execution.adaptive.{AdaptiveSparkPlanExec, BroadcastQueryStageExec}
+import org.apache.spark.sql.execution.adaptive.{AdaptiveSparkPlanExec, BroadcastQueryStageExec, QueryStageExec}
+import org.apache.spark.sql.execution.aggregate.HashAggregateExec
 import org.apache.spark.sql.execution.datasources.parquet.ParquetFileFormat
 import org.apache.spark.sql.execution.exchange.{BroadcastExchangeExec, ReusedExchangeExec, ShuffleExchangeExec}
 import org.apache.spark.sql.execution.joins.{BroadcastHashJoinExec, BroadcastNestedLoopJoinExec, CartesianProductExec, SortMergeJoinExec}
@@ -1149,6 +1150,68 @@ class CometExecSuite extends CometTestBase {
     spark.sessionState.functionRegistry.dropFunction(funcId_bloom_filter_agg)
   }
 
+  test("bloom_filter_agg - Spark partial / Comet final merge") {
+    // This test exercises the merge_filter() fix that handles Spark's full serialization
+    // format (12-byte header + bits) when merging from Spark partial to Comet final aggregates.
+    val funcId_bloom_filter_agg = new FunctionIdentifier("bloom_filter_agg")
+    spark.sessionState.functionRegistry.registerFunction(
+      funcId_bloom_filter_agg,
+      new ExpressionInfo(classOf[BloomFilterAggregate].getName, "bloom_filter_agg"),
+      (children: Seq[Expression]) =>
+        children.size match {
+          case 1 => new BloomFilterAggregate(children.head)
+          case 2 => new BloomFilterAggregate(children.head, children(1))
+          case 3 => new BloomFilterAggregate(children.head, children(1), children(2))
+        })
+
+    // Helper to count operators in plan
+    def countOperators(plan: SparkPlan, opClass: Class[_]): Int = {
+      stripAQEPlan(plan).collect {
+        case stage: QueryStageExec =>
+          countOperators(stage.plan, opClass)
+        case op if op.getClass.isAssignableFrom(opClass) => 1
+      }.sum
+    }
+
+    withParquetTable(
+      (0 until 1000)
+        .map(_ => (Random.nextInt(1000), Random.nextInt(100))),
+      "tbl") {
+
+      withSQLConf(
+        // Disable Comet partial aggregates to force Spark partial / Comet final scenario
+        CometConf.COMET_ENABLE_PARTIAL_HASH_AGGREGATE.key -> "false",
+        CometConf.COMET_EXEC_AGGREGATE_ENABLED.key -> "true",
+        CometConf.COMET_EXEC_SHUFFLE_ENABLED.key -> "true") {
+
+        val df = sql(
+          "SELECT bloom_filter_agg(cast(_2 as long), cast(1000 as long)) FROM tbl GROUP BY _1")
+
+        // Verify the query executes successfully (tests merge_filter compatibility)
+        checkSparkAnswer(df)
+
+        // Verify we have Spark partial aggregates and Comet final aggregates
+        val plan = stripAQEPlan(df.queryExecution.executedPlan)
+        val sparkPartialAggs = plan.collect {
+          case agg: HashAggregateExec if agg.aggregateExpressions.exists(_.mode == Partial) => agg
+        }
+        val cometFinalAggs = plan.collect {
+          case agg: CometHashAggregateExec if agg.aggregateExpressions.exists(_.mode == Final) =>
+            agg
+        }
+
+        assert(
+          sparkPartialAggs.nonEmpty,
+          s"Expected Spark partial aggregates but found none. Plan: $plan")
+        assert(
+          cometFinalAggs.nonEmpty,
+          s"Expected Comet final aggregates but found none. Plan: $plan")
+      }
+    }
+
+    spark.sessionState.functionRegistry.dropFunction(funcId_bloom_filter_agg)
+  }
+
   test("sort (non-global)") {
     withParquetTable((0 until 5).map(i => (i, i + 1)), "tbl") {
       val df = sql("SELECT * FROM tbl").sortWithinPartitions($"_1".desc)