diff --git a/crates/data-generation/src/storage/s3.rs b/crates/data-generation/src/storage/s3.rs
index 4c79522c..acf6fbcc 100644
--- a/crates/data-generation/src/storage/s3.rs
+++ b/crates/data-generation/src/storage/s3.rs
@@ -103,14 +103,11 @@ impl S3Storage {
         }
     }
 
-    pub(crate) fn batch_metadata_object_path(&self, table_name: &str, batch_id: u64) -> ObjectPath {
+    pub(crate) fn table_metadata_object_path(&self, table_name: &str) -> ObjectPath {
         if self.prefix.is_empty() {
-            ObjectPath::from(format!("{table_name}/batch-{batch_id:06}.metadata.json"))
+            ObjectPath::from(format!("{table_name}/metadata.json"))
         } else {
-            ObjectPath::from(format!(
-                "{}/{table_name}/batch-{batch_id:06}.metadata.json",
-                self.prefix
-            ))
+            ObjectPath::from(format!("{}/{table_name}/metadata.json", self.prefix))
         }
     }
 
@@ -119,7 +116,7 @@ impl S3Storage {
         table_name: &str,
         batch_id: u64,
     ) -> anyhow::Result<BatchOperation> {
-        let metadata_path = self.batch_metadata_object_path(table_name, batch_id);
+        let metadata_path = self.table_metadata_object_path(table_name);
         let get_result = match self.store.get(&metadata_path).await {
             Ok(r) => r,
             Err(object_store::Error::NotFound { .. }) => return Ok(BatchOperation::Insert),
@@ -127,7 +124,14 @@ impl S3Storage {
         };
 
         let bytes = get_result.bytes().await?;
-        let json: serde_json::Value = serde_json::from_slice(&bytes)?;
+        let table_meta: serde_json::Value = serde_json::from_slice(&bytes)?;
+
+        // Look up the batch entry (keyed by batch_id string) under "batches".
+        let batch_key = batch_id.to_string();
+        let json = match table_meta.get("batches").and_then(|b| b.get(&batch_key)) {
+            Some(entry) => entry,
+            None => return Ok(BatchOperation::Insert),
+        };
 
         let op = json
             .get("operation")
@@ -139,14 +143,16 @@ impl S3Storage {
         let parse_key_columns = || -> anyhow::Result<Vec<String>> {
             let Some(keys_value) = json.get("key_columns") else {
                 anyhow::bail!(
-                    "Missing 'key_columns' in metadata sidecar for {}",
-                    metadata_path
+                    "Missing 'key_columns' in metadata for table '{}' batch {}",
+                    table_name,
+                    batch_id
                 );
             };
             let Some(keys) = keys_value.as_array() else {
                 anyhow::bail!(
-                    "Invalid 'key_columns' (expected string array) in metadata sidecar for {}",
-                    metadata_path
+                    "Invalid 'key_columns' (expected string array) in metadata for table '{}' batch {}",
+                    table_name,
+                    batch_id
                 );
             };
 
@@ -155,8 +161,9 @@ impl S3Storage {
                 .map(|v| {
                     v.as_str().map(ToOwned::to_owned).ok_or_else(|| {
                         anyhow::anyhow!(
-                            "Invalid key column entry (expected string) in metadata sidecar for {}",
-                            metadata_path
+                            "Invalid key column entry (expected string) in metadata for table '{}' batch {}",
+                            table_name,
+                            batch_id
                         )
                     })
                 })
@@ -164,8 +171,9 @@ impl S3Storage {
 
             if parsed.is_empty() {
                 anyhow::bail!(
-                    "'key_columns' cannot be empty in metadata sidecar for {}",
-                    metadata_path
+                    "'key_columns' cannot be empty in metadata for table '{}' batch {}",
+                    table_name,
+                    batch_id
                 );
             }
 
@@ -181,8 +189,9 @@ impl S3Storage {
                 key_columns: parse_key_columns()?,
             }),
             other => anyhow::bail!(
-                "Unsupported operation '{other}' in metadata sidecar for {}",
-                metadata_path
+                "Unsupported operation '{other}' in metadata for table '{}' batch {}",
+                table_name,
+                batch_id
             ),
         }
     }
@@ -269,9 +278,20 @@ impl DataStorage for S3Storage {
         batch_id: u64,
         operation: &BatchOperation,
     ) -> anyhow::Result<()> {
-        let path = self.batch_metadata_object_path(table_name, batch_id);
+        let path = self.table_metadata_object_path(table_name);
+
+        // Read existing table-level metadata (if any) so we can merge.
+        let mut table_meta = match self.store.get(&path).await {
+            Ok(r) => {
+                let bytes = r.bytes().await?;
+                serde_json::from_slice::<serde_json::Value>(&bytes)
+                    .unwrap_or_else(|_| serde_json::json!({ "batches": {} }))
+            }
+            Err(object_store::Error::NotFound { .. }) => serde_json::json!({ "batches": {} }),
+            Err(e) => return Err(e.into()),
+        };
 
-        let value = match operation {
+        let batch_entry = match operation {
             BatchOperation::Insert => serde_json::json!({
                 "operation": "insert"
             }),
@@ -285,7 +305,18 @@ impl DataStorage for S3Storage {
             }),
         };
 
-        let bytes = serde_json::to_vec(&value)?;
+        // Ensure the "batches" object exists and insert/update the entry.
+        let batches = table_meta
+            .as_object_mut()
+            .expect("table metadata should be an object")
+            .entry("batches")
+            .or_insert_with(|| serde_json::json!({}));
+        batches
+            .as_object_mut()
+            .expect("batches should be an object")
+            .insert(batch_id.to_string(), batch_entry);
+
+        let bytes = serde_json::to_vec_pretty(&table_meta)?;
         self.store.put(&path, PutPayload::from(bytes)).await?;
         Ok(())
     }