The Estadio de los Juegos Mediterraneos outfit currently sit three places off the foot of the table, although they are level on points with Cordoba, Deportivo la Coruna and Elche beneath them.
Francisco - appointed in June 2013 - narrowly preserved Almeria's top-flight status last season, but has overseen a run of eight matches without a win in the Spanish top flight this this term, with their most recent victory coming at Deportivo in September.
That poor sequence culminated in a 5-2 thumping at Eibar on Monday - a result that proved to be the final straw for the Almeria board.
In a statement on the club's website on Tuesday, Almeria paid tribute to their outgoing boss.
"The club wants to publicly thank Francisco for his professionalism, commitment and dedication to the club, with which he has been linked for many years, first as a player and then as coach of both the reserves and the first team," it read.
Sergio Pardo will take temporary charge of training while a successor is sought, with Almeria set to host La Liga leaders Real Madrid - who have won 18 consecutive games in all competitions - on Friday.
