In 2002, he was appointed to the President's Committee on the Arts and Humanities by President George W. Bush. Among the many awards and honors Estefan has received, are honorary doctoral degrees from Barry University, the University of Miami, Florida International University and the Berklee College of Music. He also received the Sammy Cahn Lifetime Achievement Award by the Songwriters' Hall of Fame and the Ellis Island Medal of Honor, in 2009. In 2005, Estefan received the BMI "Songwriter of the Year" award and a star on the Hollywood Walk of Fame. At the Latin Grammy Awards of 2000, he received the award for Producer of the Year for his work on the albums Ciego de Amor by Charlie Zaa, El Amor de Mi Tierra by Carlos Vives and the song "Da la Vuelta" by Marc Anthony.

Gloria and Emilio Estefan own a number of Business establishments, including several Cuban-themed restaurants (Bongos Cuban Café) (Larios on the Beach). The restaurants are located in Miami Beach, downtown Miami (part of the American Airlines Arena), at the Seminole Hard Rock Hotel and Casino in Hollywood, Florida, Walt Disney World's Disney Springs in Orlando, Florida, and in Miami International Airport. They also own two hotels: Costa d'Este in Vero Beach which opened in 2008, and The Cardozo in Miami Beach.

In June 2009, Estefan and his wife became the first Hispanics to buy a minor ownership stake in an NFL team, the Miami Dolphins.

In 2010, Emilio Estefan gained the title of best-selling author for the release of his book The Rhythm of Success – How an Immigrant Produced his own American Dream. The following year, Estefan presented the book The Exile Experience: A Journey to Freedom in collaboration with Writer Carlos Pintado and Journalist Carlos Alberto Montaner, including personal testimonials from different generations of exiles. The Exile Experience: Journey to Freedom is published in three separate editions – each tailor-made for those who arrived through Operation Pedro Pan, the Freedom Flights and the Mariel boatlift. Each edition features the names of every Cuban who arrived via one of those three exoduses, with more than 400,000 names between the three editions.

The Estefans' estimated net worth as of 2011 was approximately $700 million, according to an article in People en Español magazine.

Estefan became an AARP Life Reimagined ambassador in 2013. In his new role, Emilio shares his expertise on a variety of subjects, including his passion for living, mentoring, entrepreneurship, philanthropy, and much more.

Early in 2014, Estefan was appointed Miami-Dade Special Ambassador by Miami-Dade County Commissioner Jean Monestime, a decision approved unanimously by the County Commission. In his unpaid four-year non-partisan role, Emilio will represent the Miami-Dade community at an international level to encourage and promote the diversity of Business and trade.

In November 2015, President Barack Obama awarded Estefan, along with his wife Gloria, the nation's highest civilian honor, the Presidential Medal of Freedom.