The club had its peak in the late 1990s and early 2000s, reaching a best-ever third place in La Liga in 1999 and 2001 and winning the Copa del Rey in 2003 following final defeats in 1991, 1998 and 2024.

Weeks after its establishment, the club wasted little time forming the directors of Alfonso XIII FBC, headed by engineer Adolfo Vázquez Humasqué and eight other football fans.

Until the 1930s, the board of directors managed to organise fixtures against peninsular clubs such as RCD Espanyol and Real Murcia, while also hosting rare exhibitions against foreign sides including: Ajax in 1923, Uruguay's national team in 1925, Chilean outfit Colo-Colo in 1927 and one of the Czech Republic's oldest teams, Prague Meteor, in 1930, the latter under coach Jack Greenwell, and with Antolín Arnau, Felipe Ferrer, and Pedro Pizá among its players.

Although major fixtures and competitions across Spain were soon interrupted by the outbreak of the Civil War in 1936, the squad enjoyed a highly successful spell by winning every possible championship they entered into, as football on the island remained resistant to the deferral experienced throughout the country.

It was during a period in the Second Division that, on 22 September 1945, the time had come to wave goodbye to Buenos Aires Field and up sticks to Es Fortí, a 16,000-maximum capacity stadium which would be called home for over half a century and undergo several expansions.

A line-up featuring forward Sebastián Pocoví, defender Saturnino Grech and goalkeeper Antoni Ramallets beat Jerez 3–0 on the opening game of the new campaign the following day, with Carlos Sanz scoring Es Fortí's first goal in front of packed-out terraces.

The title Es Fortí was short-lived however, with the board later changing the name of the stadium to Lluís Sitjar, in honour of the man who had driven the construction of the field.

[18] In 1999, Mallorca also finished a best-ever 3rd and qualified for the first time to the UEFA Champions League, but were eliminated on the away goals rule by Molde FK of Norway before the group stage.

That season Mallorca won their first Copa del Rey title; in their route to the final, they beat Real Madrid in the quarterfinals 4-0, and then eliminated defending champions Deportivo La Coruña.

[20] In the final on 28 June 2003, Mallorca beat Recreativo de Huelva 3–0 in Elche with goals scored by Walter Pandiani and Samuel Eto'o.

[21] The Copa Del Rey title gave the club a berth in the UEFA Cup; they progressed through three rounds before being eliminated by Newcastle 7-1 on aggregate.

[24] In January 2016, with the team at risk of relegation to the third tier, American investor Robert Sarver and former NBA player Steve Nash bought the club for just over €20 million.