The total penalty was £1.8 million, reduced by about £300,000 that Andrew was due for surrendering his 75-year lease early within its first 25 years.
The Crown Estate said it paid Andrew nothing at the end of the lease and received the full net amount owed as the tenancy formally ended in October.
Andrew left Royal Lodge in February amid renewed scrutiny over his links to Jeffrey Epstein, later moving to Sandringham with the King covering his upkeep and accommodation.
The 30-room Windsor mansion has no new royal occupant planned, and the Crown Estate says it will now seek a commercial use that generates value for the nation.