Mongoengine unique_with

You can specify indexes in the meta dict of the class

meta = {
    'indexes': [
        {'fields': ('merchant_id', 'order_id'), 'unique': True}
    ]
}

If you want to modify an existing index's parameters, you have to drop the index first and then recreate it. Of course you cannot create a unique index on collections that contain duplicates. Either you must remove the duplicates first, or use the 'dropDups' index creation option.