diff --git a/lib/extensions.ml b/lib/extensions.ml
index 1606e44..672b9f9 100644
--- a/lib/extensions.ml
+++ b/lib/extensions.ml
@@ -71,14 +71,14 @@ end
 
 module ChunkKeyEncoding = struct
   type kind = Default | V2
-  type t = {name : kind; sep : string}
+  type t = {name : kind; sep : string; is_default : bool}
 
   let create = function
-    | `Dot -> {name = Default; sep = "."}
-    | `Slash -> {name = Default; sep = "/"}
+    | `Dot -> {name = Default; sep = "."; is_default = false}
+    | `Slash -> {name = Default; sep = "/"; is_default = false}
 
   (* map a chunk coordinate index to a key. E.g, (2,3,1) maps to c/2/3/1 *)
-  let encode {name; sep} index =
+  let encode {name; sep; _} index =
     let f i acc =
       string_of_int i :: acc
     in
@@ -95,31 +95,37 @@ module ChunkKeyEncoding = struct
         Array.fold_right f index []
 
   let ( = ) x y =
-    x.name = y.name && x.sep = y.sep
+    x.name = y.name && x.sep = y.sep && x.is_default = y.is_default
 
-  let to_yojson {name; sep} =
+  let to_yojson {name; sep; is_default} =
     let str =
       match name with
       | Default -> "default"
       | V2 -> "v2"
     in
-    `Assoc
-    [("name", `String str)
-    ;("configuration", `Assoc [("separator", `String sep)])]
+    if is_default then
+      `Assoc [("name", `String str)]
+    else
+      `Assoc
+      [("name", `String str)
+      ;("configuration", `Assoc [("separator", `String sep)])]
 
   let of_yojson x =
     match
-      Util.get_name x,
-      Yojson.Safe.Util.(member "configuration" x |> to_assoc)
+      Util.get_name x, Yojson.Safe.Util.member "configuration" x
     with
-    | "default", [("separator", `String "/")] ->
-      Ok {name = Default; sep = "/"}
-    | "default", [("separator", `String ".")] ->
-      Ok {name = Default; sep = "."}
-    | "v2", [("separator", `String "/")] ->
-      Ok {name = V2; sep = "/"}
-    | "v2", [("separator", `String ".")] ->
-      Ok {name = V2; sep = "."}
+    | "default", `Null ->
+      Ok {name = Default; sep = "/"; is_default = true}
+    | "default", `Assoc [("separator", `String "/")] ->
+      Ok {name = Default; sep = "/"; is_default = false}
+    | "default", `Assoc [("separator", `String ".")] ->
+      Ok {name = Default; sep = "."; is_default = false}
+    | "v2", `Null ->
+      Ok {name = V2; sep = "."; is_default = true}
+    | "v2", `Assoc [("separator", `String "/")] ->
+      Ok {name = V2; sep = "/"; is_default = false}
+    | "v2", `Assoc [("separator", `String ".")] ->
+      Ok {name = V2; sep = "."; is_default = false}
     | _ -> Error "Invalid chunk key encoding configuration."
 end
 
diff --git a/test/test_metadata.ml b/test/test_metadata.ml
index 99abce2..e1d6dfc 100644
--- a/test/test_metadata.ml
+++ b/test/test_metadata.ml
@@ -183,8 +183,7 @@ let test_encode_decode_fill_value fv =
     "fill_value": %s,
     "chunk_grid":
       {"name": "regular", "configuration": {"chunk_shape": [100, 10]}},
-    "chunk_key_encoding":
-      {"name": "default", "configuration": {"separator": "."}},
+    "chunk_key_encoding": {"name": "default"},
     "attributes": {"question": 7}}|} fv
   in
   let expected = Yojson.Safe.from_string str in
@@ -267,8 +266,7 @@ let array = [
     "zarr_format": 3,
     "shape": [10000, 1000],
     "data_type": "float64",
-    "chunk_key_encoding":
-      {"name": "v2", "configuration": {"separator": "."}},
+    "chunk_key_encoding": {"name": "v2"},
     "codecs": [
       {"name": "bytes", "configuration": {"endian": "big"}}],
     "fill_value": "0x7fc00000",
@@ -340,8 +338,7 @@ let array = [
     "node_type": "array",
     "shape": [10000, 1000],
     "data_type": "float64",
-    "chunk_key_encoding":
-      {"name": "v2", "configuration": {"separator": "."}},
+    "chunk_key_encoding": {"name": "v2"},
     "codecs": 
       {"name": "bytes", "configuration": {"endian": "big"}},
     "fill_value": "0x7fc00000",
@@ -469,6 +466,34 @@ let array = [
     ~str:(template {|"UNKNOWN"|} {|[2, 4]|})
     ~msg:"Invalid Chunk grid name or configuration.";
 
+  (* test if decoding a chunk  key encoding field without a configuration
+     leads to a default value being used. *)
+  let str = {|{
+    "zarr_format": 3,
+    "shape": [10000, 1000],
+    "node_type": "array",
+    "data_type": "float64",
+    "codecs": [
+      {"name": "bytes", "configuration": {"endian": "big"}}],
+    "fill_value": "0x7fc00000",
+    "chunk_grid":
+      {"name": "regular", "configuration": {"chunk_shape": [10, 10]}},
+    "chunk_key_encoding": {"name": "v2"}}|} in
+  (match ArrayMetadata.of_yojson @@ Yojson.Safe.from_string str with
+  | Ok meta ->
+    (* we except it to use the default "." separator. *)
+    assert_equal
+      ~printer:Fun.id "2.0.1" @@ ArrayMetadata.chunk_key meta [|2; 0; 1|];
+    (* we expect the default (unspecified) config seperator to be
+       dropped when serializing the metadata to JSON format. *)
+    assert_equal
+      ~printer:Fun.id
+      Yojson.Safe.(from_string str |> to_string) @@
+      ArrayMetadata.encode meta;
+  | Error _ ->
+    assert_failure
+      "Decoding a well formed array JSON metadata should not fail.");
+
   (* test if the decoding fails if chunk key encoding contains unknown
    * separator or name. *)
   let str = {|{