diff --git a/server/src/main/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializer.java b/server/src/main/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializer.java
index 7c3e31f89..9210db599 100644
--- a/server/src/main/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializer.java
+++ b/server/src/main/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializer.java
@@ -15,8 +15,6 @@
  */
 package com.linecorp.centraldogma.server.metadata;
 
-import static com.google.common.collect.ImmutableMap.toImmutableMap;
-
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Map;
@@ -29,6 +27,8 @@
 import com.fasterxml.jackson.databind.DeserializationContext;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
+import com.google.common.collect.ImmutableMap;
+import com.google.common.collect.ImmutableMap.Builder;
 
 import com.linecorp.centraldogma.common.RepositoryRole;
 import com.linecorp.centraldogma.internal.Jackson;
@@ -94,7 +94,16 @@ private static RepositoryRole repositoryRole(Collection<Permission> permissions)
     }
 
     private static Map<String, RepositoryRole> convert(Map<String, Collection<Permission>> permissions) {
-        return permissions.entrySet().stream()
-                          .collect(toImmutableMap(Entry::getKey, entry -> repositoryRole(entry.getValue())));
+        final Builder<String, RepositoryRole> builder = ImmutableMap.builder();
+        for (Entry<String, Collection<Permission>> entry : permissions.entrySet()) {
+            final Collection<Permission> value = entry.getValue();
+            if (!value.isEmpty()) {
+                final RepositoryRole repositoryRole = repositoryRole(value);
+                assert repositoryRole != null;
+                builder.put(entry.getKey(), repositoryRole);
+            }
+        }
+
+        return builder.build();
     }
 }
diff --git a/server/src/test/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializerTest.java b/server/src/test/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializerTest.java
index 4f30e5855..279bd7d4c 100644
--- a/server/src/test/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializerTest.java
+++ b/server/src/test/java/com/linecorp/centraldogma/server/metadata/RepositoryMetadataDeserializerTest.java
@@ -45,12 +45,14 @@ void deserializeLegacyFormat() throws Exception {
                               "    \"bar@dogma.com\": [" +
                               "      \"READ\"," +
                               "      \"WRITE\"" +
-                              "    ]" +
+                              "    ]," +
+                              "    \"emptyMember\": []" + // Will be removed
                               "  }," +
                               "  \"perTokenPermissions\": {" +
                               "    \"goodman\": [" +
                               "      \"READ\"" +
-                              "    ]" +
+                              "    ]," +
+                              "    \"emptyToken\": []" + // Will be removed
                               "  }," +
                               "  \"creation\": {" +
                               "    \"user\": \"minu.song@dogma.com\"," +