Disclosed herein are methods and systems for secure data comparison using data clean rooms. In an embodiment, a computer system generates a replica database based on a provider database, which stores a cross reference table that cross references a client dataset of a client database and a provider dataset of the provider database. The system receives, at the replica database, a table that is generated by the client database using the cross-reference table. The system transmits, from the replica database, the table to the provider database. The system receives, at the replica database, a results dataset that is generated by the provider database by applying a database statement to the provider database using the table generated by the client database. The system shares, from the replica database, the results dataset with the client database.