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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 sheikh Abdullah 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. In November, however, 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.

Under "The caretaker" in charge, it was decided to discard players of the squad and strengthen with players like centre back Martín Demichelis and midfielder Júlio Baptista. After a record five consecutive La Liga wins, alongside a draw against Athletic Bilbao at San Mamés at the start of January 2011, helped the team maintain momentum in the league, finishing the 2010–11 season in 11th place.

In preparation for the 2011–12 season, the club signed with Nike as supplier of the club's kits. Málaga also reached a collaboration agreement with UNESCO, which, in addition, became the principal sponsor of the club's kit. The more prominent signings of that season were the Dutchman Ruud van Nistelrooy, the ex-Lyon French midfielder, Jérémy Toulalan, and the most expensive signing in the club's history, Santi Cazorla, who arrived from Villarreal in a €21 million deal. Other less prominent players like Isco, former Spanish international midfielder Joaquín and left back Nacho Monreal, were key in the successful season which followed for Málaga, where the club qualified for first time in its history for the Champions League after finishing the 2011–12 La Liga campaign in fourth. In their first ever participation in the Champions League, Málaga were paired with Italian giants AC Milan and reigning Belgian and Russian champions Anderlecht and Zenit St. Petersburg, respectively. Malaga made it out of the group stage unbeaten, winning against all three clubs. In the Round of 16, the team drew Portuguese champions 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, seemingly ensuring Málaga's place in the semi-finals, but two late goals by Marco Reus (90+1th minute) and Felipe Santana (90+3th minute) turned the table in favour of the home team. Immediately after the elimination, club President Abdullah ben Nasser Al Thani announced a formal complaint would be filed with 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.