The data: MongoDB Enterprise > db.coll2.find() { "_id" : ObjectId("58e6cf4badef354b4b538a00"), "name" : "jam", "a" : { "b" : [ 1 ], "c" : [ 11 ] } } { "_id" : ObjectId("58e6cf77adef354b4b538a01"), "name" : "jam", "a" : { "b" : [ 2, 3 ] } } { "_id" : ObjectId("58e6cf83adef354b4b538a02"), "name" : "jam", "a" : { "c" : [ 12 ] } } { "_id" : ObjectId("58e6cfb6adef354b4b538a03"), "name" : "jam", "a" : { "c" : [ ] } } { "_id" : ObjectId("58e6cfbdadef354b4b538a04"), "name" : "jam", "a" : { "b" : [ ] } } { "_id" : ObjectId("58e700b8adef354b4b538a05"), "name" : "jam2" } { "_id" : ObjectId("58e701edadef354b4b538a06"), "name" : "jam3", "a" : 34 } { "_id" : ObjectId("58e70244adef354b4b538a07"), "name" : "jam3", "a" : { "b" : 34 } } The indexes: MongoDB Enterprise > db.coll2.getIndexes() [ { "v" : 1, "key" : { "_id" : 1 }, "name" : "_id_", "ns" : "test.coll2" }, { "v" : 1, "key" : { "a.b.0" : 1 }, "name" : "a.b.0_1", "ns" : "test.coll2" }, { "v" : 1, "key" : { "a.c.0" : 1 }, "name" : "a.c.0_1", "ns" : "test.coll2" } ] WRONG Result of search (looking non empty array entr(ies) in the indexed sub-documents) : MongoDB Enterprise > db.coll2.find({$or :[{"a.b" : {$gt : []}}, {"a.c" :{$gt : []}}] }) MongoDB Enterprise > The result returns 0 entries. If remove the indexes using db.coll2.dropIndexes() and conduct the search again I get the RIGHT result as : MongoDB Enterprise > db.coll2.find({$or :[{"a.b" : {$gt : []}}, {"a.c" :{$gt : []}}] }) { "_id" : ObjectId("58e6cf4badef354b4b538a00"), "name" : "jam", "a" : { "b" : [ 1 ], "c" : [ 11 ] } } { "_id" : ObjectId("58e6cf77adef354b4b538a01"), "name" : "jam", "a" : { "b" : [ 2, 3 ] } } { "_id" : ObjectId("58e6cf83adef354b4b538a02"), "name" : "jam", "a" : { "c" : [ 12 ] } }