The Santander-born coach arrived at Nervión in January 1999 to replace Fernando Castro Santos at the helm of the Sevilla FC first team, when they were hovering around the mid-table positions. Under Marcos Alonso, Sevilla enjoyed an excellent second half of the season, which ended with a dramatic match in Malaga, where a victory would give the club the chance to play for promotion to the First Division against Villarreal. That memorable match would mean Sevilla FC's return to the top flight.
Marcos Alonso's tenure as coach of the Nervion side came to an end in March 2000, after the 27th matchday of the league season, when the Sevillian side were at the bottom of the table and practically doomed to relegation. His replacement was Juan Carlos Álvarez, who took charge of the Sevilla bench for the third time.