In their first campaign of 92/93, they played in Group 9 of the 3rd Division achieving promotion into Segunda B. The following season 93/94 posed financial problems for the team and they were relegated back to the 3rd Division and were at the point of disappearing from the football scene, when in 94/95 Federico Beltron and Fernando Puche came to their rescue financially.

The club did their apprenticeship in the Third and then the Second Division during 1994 and 1998 and made the jump to the First Division at the end of the 1998/99 season. They consolidated their position and comfortably held on to their First Division place in 1999/2000. In 2000/2001 right until the last moment they fought for the right to play in the UEFA.

During 2001/2002 there were many changes. Fernando Puche left and the Club's Presidency was taken over by Serafin Roldan, who is also the biggest shareholder. Malaga had to, once again, learn to become a united team as some of their key players had been sold to fund the Club. With the continued help of Manager Joaquin Peiro, the team gelled and played some remarkable football. So much so they earned a place in the Intertoto, and undefeated in this competition, won a place in the UEFA, seeded 25th.

Season 2002/3 saw the team playing some attractive football, and in the UEFA cup beat the likes of Leeds United and AEK Athens to reach the quarter finals, where they bowed out to Boavista. The club finished a respectable 13th in the league but once again faced key players leaving during the close season, and the manager Peiro was replaced by Juande Ramos.

The last two seasons has seen the club finish a respectable mid table, but there was a scare last season when up until Christmas it looked like Malaga were certs for the drop as manager Manzana struggled to find any sort of form for his team. He was replaced in January by the B team coach Antonio Tapia who worked wonders to get the team playing well again and climbing up to a tenth place finish. In fact the overall form of the side for the second half of the season, since Tapia took over, was only bettered by three clubs in the league.

During the 2005 close season the club lost the great midfield skills of Miguel Angel to rivals Real Betis and loan signing and prolific goalscorer Baiano decided to join Celta, but Tapia made some very promising signings, including the return of Salva, who was second top scorer in the whole league with Malaga two seasons ago. During the transfer window, two skillful Brazilians were signed, Bóvio and Gabriel, in the quest for Primera Liga survival, because unfortunately things didn't go the way anyone had hoped. Tapia was sacked in January 2006 after a long run of poor form that saw the club drop into the bottom three places in the league. The inexperienced Director of Football, Manolo Hierro replaced him, and has unfortunately been unable to save the club from relegation to Segunda. A sad situation that should never been allowed to happen by the owners of the club.

In huge financial difficulty, the club was put up for sale by Roldán in the summer of 2006, the main interested party for a while was the Real Estate company Unicasa together with Málaga businessmen, but Ex Real Madrid Presdient Lorenzo Sanz emerged as the new owner, purchasing for 6m and taking on the club's 30 million euro debts. His son Fernando resigned as club captain, retired from playing and was placed as the new President. The Sanz family then set about making much needed changes to the way the club is run and bringing in new players. So Málaga CF moved into new era with a great new stadium.

However, Fernando Sanz's first season was a troubled one. With the club owing so much money, they went into a form of administration to help with the crippling debts, and as a result high wage earning players had to be sold or loaned out, and Málaga were left to struggle through the season 2006/7 with a lack of top quality players. Muñiz took over from Alonso as manager in October, but the side spent the second half of the season trying to avoid relegation, which they did so, gaining a necessary point from the penultimate game of the season to be safe.

The club's fortunes took a turn for the better during season 2007/8. Muñiz made 11 shrewd signings in the summer, all free transfers or loan players, some of the players turned out to be top quality and Málaga were never out of the top three places in La Segunda all season. A club record was set when the side won the first seven games in a row and looked fairly solid until the Christmas break. The second half of the season was very different though, form dipped and the supporters were dished up some terrible displays and shocking defeats, but despite this, Málaga gained promotion back to La Primera on the last day of the season, beating Tenerife 2-1 at home in front of a full house of 30,000 to finish in 2nd place in the league. Muñiz had already signed for Racing Santander and many fans were not too upset to see him go having almost thrown promotion away. Antonio Tapia has returned to take the manager's position, his job will be to consolidate and keep the club in La Primera, which many think he has a good chance of doing.