WiredTiger is not with 2.4 version, it works from 3.0 verison. Make sure all mongos, mongo configservers and shards are of same version. Steps to recover is: Backup mongodump all the data on all 3 shards. Drop the databases on all 3 shards.(Instead can start mongo with new datadir, So you dont have to drop database, you still have data safe ) Add the 3 shards to the cluster now(there should be no error as its empty). Then Restore the mongodump's taken from 3 shards one by one. This will recover all your data. NOTE: You can test this in some staging setup with less data and verify steps.