The great navigator's remains were returned to Portugal in 1538 but his tombstone can still be seen on the south side of the church, set in the floor with a brass rail.
You can visit his grave, but no bones lie beneath it. 
mnli hypothesis: You can visit his grave, but no bones lie beneath it.  premise: The great navigator's remains were returned to Portugal in 1538 but his tombstone can still be seen on the south side of the church, set in the floor with a brass rail.