The former Spain defender took over interim charge for the 2-2 draw with Osasuna on October 1 before the club unveiled Joaquin Caparros as Michael Laudrup's successor.
"First-team coach Miguel Angel Nadal is to leave his position on the RCD Mallorca coaching staff," read a club statement.
"Nadal informed the manager Joaquin Caparros of his decision this morning, along with the president Jaume Cladera and the vice-president Llorenc Serra Ferrer.
"Nadal had decided to postpone his decision for a few days to facilitate Joaquin Caparros' settling-in period as manager.
"Miguel Angel Nadal said his goodbyes to the first-team squad in the dressing room before the week's first training session."