Almeida was born on 15 March 1957 in São Sebastião da Pedreira, Lisbon, Portugal, the son of João Baptista de Almeida and Maria Sara Portugal. At the age of eighteen, after attending a theater course at the Lisbon Conservatory (School of Theatre and Cinema) for two years, he left Portugal to continue his studies after the Conservatory was temporarily closed following the 1974 democratic revolution. He spent a year in Vienna, moving again, in 1976, to New York City where he studied at the Lee Strasberg Theatre and Film Institute, a school for the performing arts.

After his beginning in theater, Almeida started his film career in 1982 appearing in The Soldier. His first significant role came in a 1983 film, The Honorary Consul. He made appearances in TV series such as Miami Vice, but it was some years later that he made his breakthrough, appearing in the Good Morning, Babylon, a film directed by Paolo and Vittorio Taviani that opened the Cannes Film Festival in 1987. Being fluent in six languages, Almeida continued his acting career in several countries such as Portugal, England, Spain, France, Italy, Brazil, Argentina, and Germany, working in numerous films.

Almeida has two children, a son Lourenço Gonçalves Baptista de Almeida from Cecília Gonçalves (born 1993) and a daughter Ana de Tavares Risques Baptista de Almeida, with his partner Maria Risques Pereira. He was awarded a Knighthood of the Order of Prince Henry in 1992 for his contributions to the arts.

In 1994, Almeida played Félix Cortez, a former colonel of Cuban military intelligence in the Tom Clancy thriller, Clear and Present Danger, co-starring Harrison Ford, Willem Dafoe and Anne Archer. The film debuted at number one in the box office, earning a reported $20.5 million in the United States.

Clear and Present Danger was a great success and was nominated for two Academy Awards. Later in 1994, Almeida starred in the romantic comedy Only You, in which he plays a suave Italian businessman named Giovanni. According to The New York Times, the film director and producer Norman Jewison said: “I interviewed many actors for the role…. There was one Italian actor, fairly prominent, that I met in L.A. and again in New York and in Rome. And I wanted to meet several other Italian actors in Italy.” When the production moved from Pittsburgh to Italy last fall, however, none of the country’s actors seemed right for what Jewison called “the clichéd Italian gigolo, the guy that women from the Midwest always meet.” After the interview with Almeida, Jewison recalled: “Howard Feuer, the casting director, said, ‘Joaquim’s not that tall. He’s not that handsome. He’s no Rossano Brazzi here.’ I said, ‘But listen to his voice.’ There’s a machoness. Especially when he lowers it, whispers, leans across the table and pours you another glass of wine. He can be extremely intimate with his voice.”

In 1995, Almeida appeared with Antonio Banderas and Salma Hayek in the Robert Rodriguez’s action thriller Desperado. This film is the sequel to Rodriguez’s independent film El Mariachi and the second entry in the Mexico Trilogy. Joaquim de Almeida portrays the main villain Bucho, a wealthy but casually bloodthirsty drug kingpin, who rules a seedy Mexican border town. Almeida replaced Raúl Juliá as Bucho, following Juliá’s death in 1994. Desperado was screened out of competition at the 1995 Cannes Film Festival. He won a Portuguese Golden Globe for Best Actor in his next film, the 1995 Portuguese drama Adão e Eva (Adam and Eve), where he played the main female character career rival Francisco.

In 1997 he appeared in the miniseries Nostromo and starred in the Luís Galvão Teles’ drama Elles (Women). The following year, he co-starred with Eric Roberts in the Jack Perez thriller La Cucaracha (1998). The film premiered at the Austin Film Festival where it won the Feature Film Award.

In 2001, Almeida starred in the Brazilian comedy O Xangô de Baker Street, where he plays the legendary British detective Sherlock Holmes. The film is based in a book written in 1995 by the Brazilian author Jô Soares about a case involving Sherlock Holmes and is his loyal friend Doctor Watson, who are called by the Brazilian Emperor Pedro II, to find the thief of a priceless Stradivarius owned by his lover. Due to Almeida’s good representation of the character, he won another Portuguese Golden Globe for best actor, his third, and was nominated for Cinema Brazil Grand Prize award for best actor. In 2001, he had a supporting role in the war film Behind Enemy Lines as Admiral Juan Miguel Piquet, the commander of NATO’s naval forces, starring alongside Owen Wilson and Gene Hackman. The film, based on the Mrkonjić Grad incident, is centered on the story of an American naval flight officer, played by Owen Wilson, who was shot down over Bosnia, who ends up uncovering a massacre during the Bosnian conflict.

In 2004, he starred with Daryl Hannah and Denise Richards in Yo Puta, a gritty docu-style prostitution tale, based on a bestselling book by Spaniard Isabel Pisano, that tracks the slow descent of a girl, into the sex business, which is interspersed with interviews with real-life prostitutes.

That same year, he joined the cast of 24 as Ramon Salazar, the ruthless leader of a drug cartel who is put into—and later broken out of—prison by Jack Bauer. In 2007, Joaquim de Almeida limns a brutal foreman named Baxter, in the Antonio Cuadri’s El corazón de la tierra, a heady romance with a social conscience.

In 2008, he starred in the Che: Part Two, a biographical film about an Argentine doctor-turned-international revolutionary named Ernesto Guevara. Almeida played President René Barrientos, a former Bolivian politician who served as his country’s Vice President in 1964 and as its President from 1964–69.

On 16 July 2010, Almeida was confirmed to be taking on the role of antagonist Hernan Reyes in the 2011 action film Fast Five directed by Justin Lin and co-starring Vin Diesel, Paul Walker and Dwayne Johnson.

The film took $3.8 million in receipts during launch midnight showings marking the best ever opening for a Universal title and The Fast and The Furious franchise. Fast Five became the highest-grossing film of 2011 for 15 days before being replaced on 30 May 2011.

Between 2013 and 2020, Almeida has starred in The Gilded Cage, Our Brand is Crisis, The Hitman’s Bodyguard, and Downsizing.

Since 2016, Almeida has had a starring role as drug kingpin Don Epifanio Vargas on the USA Network crime drama Queen of the South, opposite Alice Braga. The show is currently in its 5th season.