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. In December 93 there was a referendum regarding chenging the club's name to Málaga CF, which was unanimously voted for, and on 30th June 1994 the new name was made official.

The club did their apprenticeship in the Third and then the Second Division between 1994 and 1998, then under manager Joaquín Peiró 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 was 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 Cup, 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, who only stayed one season (which saw us beat Barcelona 5-1 at La Rosaleda), before he moved on to huge success at Sevilla.

The next two seasons saw the club finish a respectable mid table, but there was a scare in the 2004/5 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 climbed up to a tenth place finish. In fact the overall form of the side for the second half of that season, since Tapia had taken 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 had been second top scorer in the league with Malaga two seasons previously. During the January transfer window, two skillful Brazilians were signed, Bóvio and Gabriel, in the quest for Primera Liga survival, because unfortunately things hadn't gone 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 was unfortunately unable to save the club from relegation to La Segunda. A sad situation that should never been allowed to happen by the owners of the club.

Just as CD Mealaga had experience prior to folding in 1992, Málaga CF were now in huge financial difficulty due to the way Roldán had been running the club, and it was put up for sale in the summer of 2006. The main interested party for a while was the Real Estate company Unicasa together with Málaga businessmen, and at one time there were runours that Málaga would become a 'nursery club' for Arsenal, 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 was run and brought in new players. So Málaga CF moved into new era with a great new stadium which had been redeveloped by the City Council from 2001 to 2006.

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, 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 29,000 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 returned to take the manager's position, his job was to consolidate and keep the club in La Primera.

Tapia, with Dely Valdez as his assistant, had a somewhat miraculous season 2008/9 with Málaga. Some good season long loan signings were made during the summer of 2008, and despite being the bookies' favourites to go straight back down again with a squad that cost not much more than one million euros, Tapia's side finished in 8th place after a very exciting season.

The bookies looked like they might be right after the first four games of the season, when no goals were scored and only one point was gained, putting Málaga in 19th place in La Primera. However, after scoring at home to Valladolid at the end of September, the team seems to 'click' and from then on it was a rapid rise to flirt with the European places for the rest of the season. Just a month after being in 19th place, the club were sitting proudly in 6th spot, and apart from a couple of weeks in 11th during November and December, Málaga were never out of the top 8 from the turn of 2009. That was an amazing achievement, supported by regular 20/25,000 home crowds and some amazing away support, none other than 3,000 Malaguistas at the Bernabeu to see the exciting 4-3 defeat by Real Madrid (courtesy of course, and typically, by the ref's two controversial penalties given against us!). Other memorable moments were the wins at rivals Sevilla and Real Betis. A marvelous season in La Primera!

Tapia left at the end of season 2008/9 to go to Real Betis, and Muñiz returned from Racing to take over the manager's post again.