CD Málaga had a reserve club, founded on 25 May 1948 when CD Málaga took over a junior club, CD Santo Tomás, with the purpose of establishing a reserve team. The club was renamed Club Atlético Malagueño, reviving the name of one of the two clubs that had merged to form CD Málaga in 1933.
During the 1959–60 season, CA Malagueño and CD Málaga found themselves together in the third level. As a reserve team, the former should have been relegated. To avoid this, they separated from their parent club and registered as an independent club with the Royal Spanish Football Federation.
In 1992, when CD Málaga dissolved after financial difficulties, CA Malagueño continued playing. The 1992–93 season saw them playing in Tercera División Group 9. After a successful campaign, the club was promoted to Segunda División B. The following season, however, the club was relegated again and, facing financial difficulties, were in danger of folding. On 19 December 1993, in a referendum, the club's members voted in favour of changing names and, on 29 June 1994, CA Malagueño changed their name to Málaga Club de Fútbol S.A.D., becoming an official successor to what was previously called Club Deportivo Málaga.
In the early 2000s, Málaga were a club rich in youth and top quality players, and boasted a more modern and developed stadium. Although they never pushed for a Champions League place, Málaga were always successful under the hugely popular Joaquín Peiró.
Although steering Málaga to their second consecutive 10th-placed finish, Manzano could not prevent a lacklustre side from being relegated, and they finished bottom of the league with a paltry 24 points to their name.
Málaga began the new second division season well. However, their form dipped dramatically and for two of the remaining six weeks were in the relegation zone. Málaga managed to address this situation and survived their first Segunda season.
The 2007–08 Segunda División also began impressively, with seven straight victories. Málaga seemed to be on track for promotion but, after another slump in form, they were overtaken as leaders by Numancia. They needed a victory in their final game, at home to Tenerife, to assure promotion. Two goals from Antonio Hidalgo secured a 2–1 triumph and Málaga returned to the top flight as runners-up.
Due to the club's economic problems, the at time president Fernando Sanz found investments at Doha in Qatar to launch an ambitious project, entering in conversations with sheikhAbdullah ben Nasser Al Thani. On 11 June 2010, after week of negotiations, Al Thani became in the entity's new owner, being named president on 28 July in the members' meeting.
On 28 June 2010, Jesualdo Ferreira was appointed as coach and Moayad Shatat was appointed as a vice president and general manager. Following this was the signing of prominent players like Salomón Rondón and Eliseu. However, in November, Jesualdo was fired because he had not obtained the desired performance, positioning the club in the relegation places. Later, Shatat confirmed Manuel Pellegrini as coach.
In their first ever participation in the Champions League, Malaga were paired with Italian giants AC Milan, Belgian and Russian champions, Anderlecht and Zenit Saint Petersburg. Malaga made it out of the group stage unbeaten, winning against all three clubs. In the Round of 16, Malaga drew Portuguese champions FC Porto, losing the first away game 1–0, while winning at home 2–0, advancing to the quarter-finals. In a highly anticipated tie against German champions Borussia Dortmund, the home game ended 0–0, leaving Malagauistas with a reasonable chance to advance on the back of a draw in the away fixture. In a second leg marked by controversial referee decisions, the scoreboard showed 1–2 at the full 90 minutes mark, ensuring Malaga's place in the semi-finals, but two late goals by Marco Reus (90+1) and Felipe Santana (90+3) turned the table in favor of the home team. Immediately after the harsh elimination, club president, Abdullah Al Thani, announced a formal complaint would be filed to UEFA and FIFA.
The following season Málaga was banned by UEFA, along with other clubs for its debts, so the agency in a statement declared that the club will be excluded from a subsequent competition, for which it would otherwise qualify, in the next four seasons. However, the ban was eventually downgraded to one season and the club was excluded from the 2013–14 Europa League.
In the summer of 2013, Isco was sold to Real Madrid, Joaquín to Fiorentina and midfielder Jérémy Toulalan to Monaco. The managerial position also changed, with Bernd Schuster taking over from Manuel Pellegrini.
Between 1961 and 1983, the club organised its own summer tournament, the Trofeo Costa del Sol. In this first age of the tournament, the club won this competition themselves on three occasions, beating Real Madrid, Red Star Belgrade, and Derby County in the finals. After a long time of inactivity from 1983 onwards, the competition was revived in 2003. Since then, the club has won the competition on five occasions, beating Newcastle United, Real Betis, and Parma in the finals. All eight trophies are currently placed together in the Museo Malaguista in La Rosaleda.