diff --git a/proto/expr.proto b/proto/expr.proto
index c5c66733d0d92..4cbe7d2abb1c2 100644
--- a/proto/expr.proto
+++ b/proto/expr.proto
@@ -471,6 +471,20 @@ message AggCall {
   ExprNode scalar = 9;
 }
 
+// The aggregation type.
+//
+// Ideally this should be used to encode the Rust `AggCall::agg_type` field, but historically we
+// flattened it into multiple fields in proto `AggCall` - `kind` + `udf` + `scalar`. So this
+// `AggType` proto type is only used by `WindowFunction` currently.
+message AggType {
+  AggCall.Kind kind = 1;
+
+  // UDF metadata. Only present when the kind is `USER_DEFINED`.
+  optional UserDefinedFunctionMetadata udf_meta = 8;
+  // Wrapped scalar expression. Only present when the kind is `WRAP_SCALAR`.
+  optional ExprNode scalar_expr = 9;
+}
+
 message WindowFrame {
   enum Type {
     TYPE_UNSPECIFIED = 0;
@@ -562,7 +576,8 @@ message WindowFunction {
 
   oneof type {
     GeneralType general = 1;
-    AggCall.Kind aggregate = 2;
+    AggCall.Kind aggregate_simple = 2 [deprecated = true]; // Deprecated since we have a new `aggregate` variant.
+    AggType aggregate = 103;
   }
   repeated InputRef args = 3;
   data.DataType return_type = 4;
diff --git a/src/expr/core/src/aggregate/def.rs b/src/expr/core/src/aggregate/def.rs
index 3abe80dcd4d31..8554affb23af8 100644
--- a/src/expr/core/src/aggregate/def.rs
+++ b/src/expr/core/src/aggregate/def.rs
@@ -27,7 +27,9 @@ use risingwave_common::types::{DataType, Datum};
 use risingwave_common::util::sort_util::{ColumnOrder, OrderType};
 use risingwave_common::util::value_encoding::DatumFromProtoExt;
 pub use risingwave_pb::expr::agg_call::PbKind as PbAggKind;
-use risingwave_pb::expr::{PbAggCall, PbExprNode, PbInputRef, PbUserDefinedFunctionMetadata};
+use risingwave_pb::expr::{
+    PbAggCall, PbAggType, PbExprNode, PbInputRef, PbUserDefinedFunctionMetadata,
+};
 
 use crate::expr::{
     build_from_prost, BoxedExpression, ExpectExt, Expression, LiteralExpression, Token,
@@ -65,7 +67,7 @@ pub struct AggCall {
 
 impl AggCall {
     pub fn from_protobuf(agg_call: &PbAggCall) -> Result<Self> {
-        let agg_type = AggType::from_protobuf(
+        let agg_type = AggType::from_protobuf_flatten(
             agg_call.get_kind()?,
             agg_call.udf.as_ref(),
             agg_call.scalar.as_ref(),
@@ -160,7 +162,7 @@ impl<Iter: Iterator<Item = Token>> Parser<Iter> {
         self.tokens.next(); // Consume the RParen
 
         AggCall {
-            agg_type: AggType::from_protobuf(func, None, None).unwrap(),
+            agg_type: AggType::from_protobuf_flatten(func, None, None).unwrap(),
             args: AggArgs {
                 data_types: children.iter().map(|(_, ty)| ty.clone()).collect(),
                 val_indices: children.iter().map(|(idx, _)| *idx).collect(),
@@ -260,7 +262,7 @@ impl From<PbAggKind> for AggType {
 }
 
 impl AggType {
-    pub fn from_protobuf(
+    pub fn from_protobuf_flatten(
         pb_kind: PbAggKind,
         user_defined: Option<&PbUserDefinedFunctionMetadata>,
         scalar: Option<&PbExprNode>,
@@ -286,6 +288,35 @@ impl AggType {
             Self::WrapScalar(_) => PbAggKind::WrapScalar,
         }
     }
+
+    pub fn from_protobuf(pb_type: &PbAggType) -> Result<Self> {
+        match pb_type.kind() {
+            PbAggKind::Unspecified => bail!("Unrecognized agg."),
+            PbAggKind::UserDefined => Ok(AggType::UserDefined(pb_type.get_udf_meta()?.clone())),
+            PbAggKind::WrapScalar => Ok(AggType::WrapScalar(pb_type.get_scalar_expr()?.clone())),
+            kind => Ok(AggType::Builtin(kind)),
+        }
+    }
+
+    pub fn to_protobuf(&self) -> PbAggType {
+        match self {
+            Self::Builtin(kind) => PbAggType {
+                kind: *kind as _,
+                udf_meta: None,
+                scalar_expr: None,
+            },
+            Self::UserDefined(udf_meta) => PbAggType {
+                kind: PbAggKind::UserDefined as _,
+                udf_meta: Some(udf_meta.clone()),
+                scalar_expr: None,
+            },
+            Self::WrapScalar(scalar_expr) => PbAggType {
+                kind: PbAggKind::WrapScalar as _,
+                udf_meta: None,
+                scalar_expr: Some(scalar_expr.clone()),
+            },
+        }
+    }
 }
 
 /// Macros to generate match arms for `AggType`.
diff --git a/src/expr/core/src/window_function/kind.rs b/src/expr/core/src/window_function/kind.rs
index 32c5f746020d0..4d2f1ef00b8f6 100644
--- a/src/expr/core/src/window_function/kind.rs
+++ b/src/expr/core/src/window_function/kind.rs
@@ -51,11 +51,14 @@ impl WindowFuncKind {
                 Ok(PbGeneralType::Lead) => Self::Lead,
                 Err(_) => bail!("no such window function type"),
             },
-            PbType::Aggregate(agg_type) => match PbAggKind::try_from(*agg_type) {
+            PbType::AggregateSimple(agg_type) => match PbAggKind::try_from(*agg_type) {
                 // TODO(runji): support UDAF and wrapped scalar functions
-                Ok(agg_type) => Self::Aggregate(AggType::from_protobuf(agg_type, None, None)?),
+                Ok(agg_type) => {
+                    Self::Aggregate(AggType::from_protobuf_flatten(agg_type, None, None)?)
+                }
                 Err(_) => bail!("no such aggregate function type"),
             },
+            PbType::Aggregate(agg_type) => Self::Aggregate(AggType::from_protobuf(agg_type)?),
         };
         Ok(kind)
     }
diff --git a/src/frontend/src/binder/expr/function/mod.rs b/src/frontend/src/binder/expr/function/mod.rs
index 5d3dfb79300d2..00f2438cb35af 100644
--- a/src/frontend/src/binder/expr/function/mod.rs
+++ b/src/frontend/src/binder/expr/function/mod.rs
@@ -227,8 +227,8 @@ impl Binder {
             None
         };
 
-        let agg_type = if let Some(wrapped_agg_type) = wrapped_agg_type {
-            Some(wrapped_agg_type)
+        let agg_type = if wrapped_agg_type.is_some() {
+            wrapped_agg_type
         } else if let Some(ref udf) = udf
             && udf.kind.is_aggregate()
         {
diff --git a/src/frontend/src/optimizer/plan_node/generic/over_window.rs b/src/frontend/src/optimizer/plan_node/generic/over_window.rs
index 5622d1e8952cf..100586506d9bc 100644
--- a/src/frontend/src/optimizer/plan_node/generic/over_window.rs
+++ b/src/frontend/src/optimizer/plan_node/generic/over_window.rs
@@ -121,7 +121,7 @@ impl PlanWindowFunction {
             DenseRank => PbType::General(PbGeneralType::DenseRank as _),
             Lag => PbType::General(PbGeneralType::Lag as _),
             Lead => PbType::General(PbGeneralType::Lead as _),
-            Aggregate(agg_type) => PbType::Aggregate(agg_type.to_protobuf_simple() as _),
+            Aggregate(agg_type) => PbType::Aggregate(agg_type.to_protobuf()),
         };
 
         PbWindowFunction {