diff --git a/dandi/consts.py b/dandi/consts.py
index 535d6e986..b68dff98f 100644
--- a/dandi/consts.py
+++ b/dandi/consts.py
@@ -159,3 +159,6 @@ class DandiInstance(NamedTuple):
 
 #: Maximum number of Zarr directory entries to upload at once
 ZARR_UPLOAD_BATCH_SIZE = 255
+
+#: Maximum number of Zarr directory entries to delete at once
+ZARR_DELETE_BATCH_SIZE = 100
diff --git a/dandi/dandiapi.py b/dandi/dandiapi.py
index 7b7bff7a9..1f6341300 100644
--- a/dandi/dandiapi.py
+++ b/dandi/dandiapi.py
@@ -15,6 +15,7 @@
     ClassVar,
     Dict,
     FrozenSet,
+    Iterable,
     Iterator,
     List,
     Optional,
@@ -38,6 +39,7 @@
     DRAFT,
     MAX_CHUNK_SIZE,
     RETRY_STATUSES,
+    ZARR_DELETE_BATCH_SIZE,
     DandiInstance,
     EmbargoStatus,
     known_instances,
@@ -46,7 +48,13 @@
 from .exceptions import NotFoundError, SchemaVersionError
 from .keyring import keyring_lookup
 from .misctypes import BasePath, Digest
-from .utils import USER_AGENT, check_dandi_version, ensure_datetime, is_interactive
+from .utils import (
+    USER_AGENT,
+    check_dandi_version,
+    chunked,
+    ensure_datetime,
+    is_interactive,
+)
 
 lgr = get_logger()
 
@@ -1412,6 +1420,17 @@ def iterfiles(self, include_dirs: bool = False) -> Iterator["RemoteZarrEntry"]:
         """
         return self.filetree.iterfiles(include_dirs=include_dirs)
 
+    def rmfiles(self, files: Iterable["RemoteZarrEntry"]) -> None:
+        """Delete one or more files from the Zarr"""
+        # Don't bother checking that the entries are actually files or even
+        # belong to this Zarr, as if they're not, the server will return an
+        # error anyway.
+        for entries in chunked(files, ZARR_DELETE_BATCH_SIZE):
+            self.client.delete(
+                f"/zarr/{self.zarr}/files/",
+                json=[{"path": str(e)} for e in entries],
+            )
+
 
 class RemoteAsset(BaseRemoteAsset):
     """
diff --git a/dandi/files.py b/dandi/files.py
index 9cea3fe69..14ae9d123 100644
--- a/dandi/files.py
+++ b/dandi/files.py
@@ -833,8 +833,9 @@ def iter_upload(
                 json={"metadata": metadata, "zarr_id": zarr_id},
             )
         a = RemoteAsset.from_data(dandiset, r)
+        assert isinstance(a, RemoteZarrAsset)
         to_upload: List[dict] = []
-        to_delete: List[dict] = []
+        to_delete: List[RemoteZarrEntry] = []
         for p in stat.files:
             pdigest = p.get_digest().value
             item = {"path": str(p), "etag": pdigest}
@@ -851,8 +852,7 @@ def iter_upload(
                                 pp,
                                 p,
                             )
-                            old_zarr_entries.pop(pps)
-                            to_delete.append({"path": pps})
+                            to_delete.append(old_zarr_entries.pop(pps))
                         break
                 to_upload.append(item)
             else:
@@ -864,11 +864,9 @@ def iter_upload(
                     )
                     for ee in e.iterfiles():
                         try:
-                            old_zarr_entries.pop(str(ee))
+                            to_delete.append(old_zarr_entries.pop(str(ee)))
                         except KeyError:
                             pass
-                        else:
-                            to_delete.append({"path": str(ee)})
                     to_upload.append(item)
                 elif pdigest != e.get_digest().value:
                     lgr.debug(
@@ -880,7 +878,7 @@ def iter_upload(
                 else:
                     lgr.debug("%s: File %s already on server; skipping", asset_path, p)
         if to_delete:
-            client.delete(f"/zarr/{zarr_id}/files/", json=to_delete)
+            a.rmfiles(to_delete)
         yield {"status": "initiating upload"}
         lgr.debug("%s: Beginning upload", asset_path)
         bytes_uploaded = 0
@@ -931,17 +929,14 @@ def iter_upload(
                 lgr.debug("%s: Completing upload of batch #%d", asset_path, i)
                 client.post(f"/zarr/{zarr_id}/upload/complete/")
         lgr.debug("%s: Upload completed", asset_path)
-        old_zarr_files = [k for k, e in old_zarr_entries.items() if e.is_file()]
+        old_zarr_files = [e for e in old_zarr_entries.values() if e.is_file()]
         if old_zarr_files:
             lgr.debug(
                 "%s: Deleting %s in remote Zarr not present locally",
                 asset_path,
                 pluralize(len(old_zarr_files), "file"),
             )
-            client.delete(
-                f"/zarr/{zarr_id}/files/",
-                json=[{"path": k} for k in old_zarr_files],
-            )
+            a.rmfiles(old_zarr_files)
         r = client.get(f"/zarr/{zarr_id}/")
         if r["checksum"] != filetag:
             raise RuntimeError(