Botín was born in Santander, Cantabria, on the northern coast of Spain, the eldest of two sons of Emilio Botín y Sanz de Sautuola, born on 18 January 1903, and Ana María García de los Ríos y Caller. After attending as a boarding student the Jesuit school of Colegio de la Inmaculada, in Gijón, he studied Law and Economics at the University of Deusto in Bilbao.
Botín and his family held undisclosed bank accounts in Switzerland since 1937. Those accounts were discovered by the Spanish tax authorities in 2010. Botín and his family voluntarily settled the case, paying a bill of €200 million. In 2012, Spain's High Court dropped a tax evasion probe for these issues, stating that Botín and his family had satisfied Spanish tax authorities with the €200 million settlement.
Botín was married to the Marquise of O'Shea, and they had six children. His daughter Carmen was married to Golfer Seve Ballesteros from 1988 to 2004.
In 2005 Forbes put Emilio Botín's net worth at $1.7 billion. Botín's eldest daughter, Ana Patricia Botín, was the President of Banesto from 2002 to November 2010 and was the CEO of Santander UK from December 2010 until Emilio's death upon which she was elected his successor as President of Grupo Santander.
During his presidency, Banco Santander was named 2012 'Best bank in the world', the third time that the bank had received this award in the past seven years.
He died on 9 September 2014 of a heart attack in Madrid. Botín was survived by his six children and nineteen grandchilden.