The MongoDB database stores documents in a format called BSON, which is a binary serialization of JSON-like documents. BSON contains extensions that allow representation of data types not found in JSON, such as Date and BinData types. The MongoDB client drivers perform serialization and deserialization, allowing the database to "reach into" BSON objects for tasks like building index keys or matching against query expressions. This makes BSON a language-independent data interchange format that can be used by applications beyond just MongoDB. Additionally, BSON is more efficient than XML and JSON in terms of space and compute time, with a slightly higher overhead due to its schemaless nature compared to Protocol Buffers.