diff --git a/flow/connectors/bigquery/qrep.go b/flow/connectors/bigquery/qrep.go
index bf1c603d43..df771e50a2 100644
--- a/flow/connectors/bigquery/qrep.go
+++ b/flow/connectors/bigquery/qrep.go
@@ -47,7 +47,7 @@ func (c *BigQueryConnector) SyncQRepRecords(
 
 	avroSync := &QRepAvroSyncMethod{connector: c, gcsBucket: config.StagingPath}
 	return avroSync.SyncQRepRecords(config.FlowJobName, destTable, partition,
-		tblMetadata, stream, config.SyncedAtColName)
+		tblMetadata, stream, config.SyncedAtColName, config.SoftDeleteColName)
 }
 
 func (c *BigQueryConnector) replayTableSchemaDeltasQRep(config *protos.QRepConfig, partition *protos.QRepPartition,
diff --git a/flow/connectors/bigquery/qrep_avro_sync.go b/flow/connectors/bigquery/qrep_avro_sync.go
index 882f11a8c2..6a83d23ae8 100644
--- a/flow/connectors/bigquery/qrep_avro_sync.go
+++ b/flow/connectors/bigquery/qrep_avro_sync.go
@@ -48,7 +48,7 @@ func (s *QRepAvroSyncMethod) SyncRecords(
 			flowJobName, dstTableName, syncBatchID),
 	)
 	// You will need to define your Avro schema as a string
-	avroSchema, err := DefineAvroSchema(dstTableName, dstTableMetadata, "")
+	avroSchema, err := DefineAvroSchema(dstTableName, dstTableMetadata, "", "")
 	if err != nil {
 		return 0, fmt.Errorf("failed to define Avro schema: %w", err)
 	}
@@ -108,6 +108,7 @@ func (s *QRepAvroSyncMethod) SyncQRepRecords(
 	dstTableMetadata *bigquery.TableMetadata,
 	stream *model.QRecordStream,
 	syncedAtCol string,
+	softDeleteCol string,
 ) (int, error) {
 	startTime := time.Now()
 	flowLog := slog.Group("sync_metadata",
@@ -116,7 +117,7 @@ func (s *QRepAvroSyncMethod) SyncQRepRecords(
 		slog.String("destinationTable", dstTableName),
 	)
 	// You will need to define your Avro schema as a string
-	avroSchema, err := DefineAvroSchema(dstTableName, dstTableMetadata, syncedAtCol)
+	avroSchema, err := DefineAvroSchema(dstTableName, dstTableMetadata, syncedAtCol, softDeleteCol)
 	if err != nil {
 		return 0, fmt.Errorf("failed to define Avro schema: %w", err)
 	}
@@ -139,8 +140,11 @@ func (s *QRepAvroSyncMethod) SyncQRepRecords(
 	stmts := []string{"BEGIN TRANSACTION;"}
 
 	selector := "*"
+	if softDeleteCol != "" { // PeerDB column
+		selector += ", FALSE"
+	}
 	if syncedAtCol != "" { // PeerDB column
-		selector = "*, CURRENT_TIMESTAMP"
+		selector += ", CURRENT_TIMESTAMP"
 	}
 	// Insert the records from the staging table into the destination table
 	insertStmt := fmt.Sprintf("INSERT INTO `%s.%s` SELECT %s FROM `%s.%s`;",
@@ -187,12 +191,13 @@ type AvroSchema struct {
 func DefineAvroSchema(dstTableName string,
 	dstTableMetadata *bigquery.TableMetadata,
 	syncedAtCol string,
+	softDeleteCol string,
 ) (*model.QRecordAvroSchemaDefinition, error) {
 	avroFields := []AvroField{}
 	nullableFields := make(map[string]struct{})
 
 	for _, bqField := range dstTableMetadata.Schema {
-		if bqField.Name == syncedAtCol {
+		if bqField.Name == syncedAtCol || bqField.Name == softDeleteCol {
 			continue
 		}
 		avroType, err := GetAvroType(bqField)
diff --git a/flow/generated/protos/flow.pb.go b/flow/generated/protos/flow.pb.go
index 4be91a690f..3cb146df01 100644
--- a/flow/generated/protos/flow.pb.go
+++ b/flow/generated/protos/flow.pb.go
@@ -2671,6 +2671,7 @@ type QRepConfig struct {
 	// to be used after the old mirror is dropped
 	DstTableFullResync bool   `protobuf:"varint,18,opt,name=dst_table_full_resync,json=dstTableFullResync,proto3" json:"dst_table_full_resync,omitempty"`
 	SyncedAtColName    string `protobuf:"bytes,19,opt,name=synced_at_col_name,json=syncedAtColName,proto3" json:"synced_at_col_name,omitempty"`
+	SoftDeleteColName  string `protobuf:"bytes,20,opt,name=soft_delete_col_name,json=softDeleteColName,proto3" json:"soft_delete_col_name,omitempty"`
 }
 
 func (x *QRepConfig) Reset() {
@@ -2838,6 +2839,13 @@ func (x *QRepConfig) GetSyncedAtColName() string {
 	return ""
 }
 
+func (x *QRepConfig) GetSoftDeleteColName() string {
+	if x != nil {
+		return x.SoftDeleteColName
+	}
+	return ""
+}
+
 type QRepPartition struct {
 	state         protoimpl.MessageState
 	sizeCache     protoimpl.SizeCache
@@ -3908,7 +3916,7 @@ var file_flow_proto_rawDesc = []byte{
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@@ -3968,104 +3976,107 @@ var file_flow_proto_rawDesc = []byte{
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+	0x54, 0x45, 0x5f, 0x4d, 0x4f, 0x44, 0x45, 0x5f, 0x4f, 0x56, 0x45, 0x52, 0x57, 0x52, 0x49, 0x54,
+	0x45, 0x10, 0x02, 0x42, 0x76, 0x0a, 0x0f, 0x63, 0x6f, 0x6d, 0x2e, 0x70, 0x65, 0x65, 0x72, 0x64,
+	0x62, 0x5f, 0x66, 0x6c, 0x6f, 0x77, 0x42, 0x09, 0x46, 0x6c, 0x6f, 0x77, 0x50, 0x72, 0x6f, 0x74,
+	0x6f, 0x50, 0x01, 0x5a, 0x10, 0x67, 0x65, 0x6e, 0x65, 0x72, 0x61, 0x74, 0x65, 0x64, 0x2f, 0x70,
+	0x72, 0x6f, 0x74, 0x6f, 0x73, 0xa2, 0x02, 0x03, 0x50, 0x58, 0x58, 0xaa, 0x02, 0x0a, 0x50, 0x65,
+	0x65, 0x72, 0x64, 0x62, 0x46, 0x6c, 0x6f, 0x77, 0xca, 0x02, 0x0a, 0x50, 0x65, 0x65, 0x72, 0x64,
+	0x62, 0x46, 0x6c, 0x6f, 0x77, 0xe2, 0x02, 0x16, 0x50, 0x65, 0x65, 0x72, 0x64, 0x62, 0x46, 0x6c,
+	0x6f, 0x77, 0x5c, 0x47, 0x50, 0x42, 0x4d, 0x65, 0x74, 0x61, 0x64, 0x61, 0x74, 0x61, 0xea, 0x02,
+	0x0a, 0x50, 0x65, 0x65, 0x72, 0x64, 0x62, 0x46, 0x6c, 0x6f, 0x77, 0x62, 0x06, 0x70, 0x72, 0x6f,
+	0x74, 0x6f, 0x33,
 }
 
 var (
diff --git a/flow/workflows/snapshot_flow.go b/flow/workflows/snapshot_flow.go
index bc8448b4b7..998317c520 100644
--- a/flow/workflows/snapshot_flow.go
+++ b/flow/workflows/snapshot_flow.go
@@ -177,6 +177,7 @@ func (s *SnapshotFlowExecution) cloneTable(
 		MaxParallelWorkers:         numWorkers,
 		StagingPath:                s.config.SnapshotStagingPath,
 		SyncedAtColName:            s.config.SyncedAtColName,
+		SoftDeleteColName:          s.config.SoftDeleteColName,
 		WriteMode: &protos.QRepWriteMode{
 			WriteType: protos.QRepWriteType_QREP_WRITE_MODE_APPEND,
 		},
diff --git a/nexus/pt/src/peerdb_flow.rs b/nexus/pt/src/peerdb_flow.rs
index 50b1541e0d..4163aa0363 100644
--- a/nexus/pt/src/peerdb_flow.rs
+++ b/nexus/pt/src/peerdb_flow.rs
@@ -474,6 +474,8 @@ pub struct QRepConfig {
     pub dst_table_full_resync: bool,
     #[prost(string, tag="19")]
     pub synced_at_col_name: ::prost::alloc::string::String,
+    #[prost(string, tag="20")]
+    pub soft_delete_col_name: ::prost::alloc::string::String,
 }
 #[allow(clippy::derive_partial_eq_without_eq)]
 #[derive(Clone, PartialEq, ::prost::Message)]
diff --git a/nexus/pt/src/peerdb_flow.serde.rs b/nexus/pt/src/peerdb_flow.serde.rs
index 1ebf981cd4..3374e09b99 100644
--- a/nexus/pt/src/peerdb_flow.serde.rs
+++ b/nexus/pt/src/peerdb_flow.serde.rs
@@ -2771,6 +2771,9 @@ impl serde::Serialize for QRepConfig {
         if !self.synced_at_col_name.is_empty() {
             len += 1;
         }
+        if !self.soft_delete_col_name.is_empty() {
+            len += 1;
+        }
         let mut struct_ser = serializer.serialize_struct("peerdb_flow.QRepConfig", len)?;
         if !self.flow_job_name.is_empty() {
             struct_ser.serialize_field("flowJobName", &self.flow_job_name)?;
@@ -2831,6 +2834,9 @@ impl serde::Serialize for QRepConfig {
         if !self.synced_at_col_name.is_empty() {
             struct_ser.serialize_field("syncedAtColName", &self.synced_at_col_name)?;
         }
+        if !self.soft_delete_col_name.is_empty() {
+            struct_ser.serialize_field("softDeleteColName", &self.soft_delete_col_name)?;
+        }
         struct_ser.end()
     }
 }
@@ -2878,6 +2884,8 @@ impl<'de> serde::Deserialize<'de> for QRepConfig {
             "dstTableFullResync",
             "synced_at_col_name",
             "syncedAtColName",
+            "soft_delete_col_name",
+            "softDeleteColName",
         ];
 
         #[allow(clippy::enum_variant_names)]
@@ -2901,6 +2909,7 @@ impl<'de> serde::Deserialize<'de> for QRepConfig {
             SetupWatermarkTableOnDestination,
             DstTableFullResync,
             SyncedAtColName,
+            SoftDeleteColName,
             __SkipField__,
         }
         impl<'de> serde::Deserialize<'de> for GeneratedField {
@@ -2942,6 +2951,7 @@ impl<'de> serde::Deserialize<'de> for QRepConfig {
                             "setupWatermarkTableOnDestination" | "setup_watermark_table_on_destination" => Ok(GeneratedField::SetupWatermarkTableOnDestination),
                             "dstTableFullResync" | "dst_table_full_resync" => Ok(GeneratedField::DstTableFullResync),
                             "syncedAtColName" | "synced_at_col_name" => Ok(GeneratedField::SyncedAtColName),
+                            "softDeleteColName" | "soft_delete_col_name" => Ok(GeneratedField::SoftDeleteColName),
                             _ => Ok(GeneratedField::__SkipField__),
                         }
                     }
@@ -2980,6 +2990,7 @@ impl<'de> serde::Deserialize<'de> for QRepConfig {
                 let mut setup_watermark_table_on_destination__ = None;
                 let mut dst_table_full_resync__ = None;
                 let mut synced_at_col_name__ = None;
+                let mut soft_delete_col_name__ = None;
                 while let Some(k) = map.next_key()? {
                     match k {
                         GeneratedField::FlowJobName => {
@@ -3106,6 +3117,12 @@ impl<'de> serde::Deserialize<'de> for QRepConfig {
                             }
                             synced_at_col_name__ = Some(map.next_value()?);
                         }
+                        GeneratedField::SoftDeleteColName => {
+                            if soft_delete_col_name__.is_some() {
+                                return Err(serde::de::Error::duplicate_field("softDeleteColName"));
+                            }
+                            soft_delete_col_name__ = Some(map.next_value()?);
+                        }
                         GeneratedField::__SkipField__ => {
                             let _ = map.next_value::<serde::de::IgnoredAny>()?;
                         }
@@ -3131,6 +3148,7 @@ impl<'de> serde::Deserialize<'de> for QRepConfig {
                     setup_watermark_table_on_destination: setup_watermark_table_on_destination__.unwrap_or_default(),
                     dst_table_full_resync: dst_table_full_resync__.unwrap_or_default(),
                     synced_at_col_name: synced_at_col_name__.unwrap_or_default(),
+                    soft_delete_col_name: soft_delete_col_name__.unwrap_or_default(),
                 })
             }
         }
diff --git a/protos/flow.proto b/protos/flow.proto
index 57ceef506f..965d8d0fce 100644
--- a/protos/flow.proto
+++ b/protos/flow.proto
@@ -323,6 +323,7 @@ message QRepConfig {
   bool dst_table_full_resync = 18;
 
   string synced_at_col_name = 19;
+  string soft_delete_col_name = 20;
 }
 
 message QRepPartition {
diff --git a/ui/grpc_generated/flow.ts b/ui/grpc_generated/flow.ts
index 094d97765a..1ba651b45f 100644
--- a/ui/grpc_generated/flow.ts
+++ b/ui/grpc_generated/flow.ts
@@ -431,6 +431,7 @@ export interface QRepConfig {
    */
   dstTableFullResync: boolean;
   syncedAtColName: string;
+  softDeleteColName: string;
 }
 
 export interface QRepPartition {
@@ -5309,6 +5310,7 @@ function createBaseQRepConfig(): QRepConfig {
     setupWatermarkTableOnDestination: false,
     dstTableFullResync: false,
     syncedAtColName: "",
+    softDeleteColName: "",
   };
 }
 
@@ -5371,6 +5373,9 @@ export const QRepConfig = {
     if (message.syncedAtColName !== "") {
       writer.uint32(154).string(message.syncedAtColName);
     }
+    if (message.softDeleteColName !== "") {
+      writer.uint32(162).string(message.softDeleteColName);
+    }
     return writer;
   },
 
@@ -5514,6 +5519,13 @@ export const QRepConfig = {
 
           message.syncedAtColName = reader.string();
           continue;
+        case 20:
+          if (tag !== 162) {
+            break;
+          }
+
+          message.softDeleteColName = reader.string();
+          continue;
       }
       if ((tag & 7) === 4 || tag === 0) {
         break;
@@ -5548,6 +5560,7 @@ export const QRepConfig = {
         : false,
       dstTableFullResync: isSet(object.dstTableFullResync) ? Boolean(object.dstTableFullResync) : false,
       syncedAtColName: isSet(object.syncedAtColName) ? String(object.syncedAtColName) : "",
+      softDeleteColName: isSet(object.softDeleteColName) ? String(object.softDeleteColName) : "",
     };
   },
 
@@ -5610,6 +5623,9 @@ export const QRepConfig = {
     if (message.syncedAtColName !== "") {
       obj.syncedAtColName = message.syncedAtColName;
     }
+    if (message.softDeleteColName !== "") {
+      obj.softDeleteColName = message.softDeleteColName;
+    }
     return obj;
   },
 
@@ -5643,6 +5659,7 @@ export const QRepConfig = {
     message.setupWatermarkTableOnDestination = object.setupWatermarkTableOnDestination ?? false;
     message.dstTableFullResync = object.dstTableFullResync ?? false;
     message.syncedAtColName = object.syncedAtColName ?? "";
+    message.softDeleteColName = object.softDeleteColName ?? "";
     return message;
   },
 };