After becoming dissatisfied with the Castro regime he joined Manuel Artime against Castro. Artime's group was supported by Frank Sturgis and the CIA as related by Fabian Escalante in CIA Covert Operations: 1959 - 1962. Sturgis flew a CIA plane over Havana dropping thousands of pamphlets urging the Cuban people to overthrow the Castro regime on October 21, 1959 as part of Artime's operations. About December 1959, Manuel Artime left Cuba with a hundred thousand pesos when nothing happened. Quintero moved to the United States the next month.
On June 5, 1960, The Movement for the Recovery of the Revolution or (MRR) was created by Manuel Artime, Tony Varona, Aureliano Arango, Jose Miro Cardona and Quintero. About the same time Quintero became a member of Operation 40 along with other anti-Castro Cubans. In 1961 Quintero secretly re-entered Cuba and was arrested just prior to the Bay of Pigs Invasion, was released and returned to the U.S.
Rafael Quintero served as deputy leader of MRR under Artime in 1962. Manuel Artime got money from the CIA through Theodore Shackley in 1963. Artime, Quintero and Felix Rodriguez moved to Nicaragua creating an army of 300 men and obtained weapons, supplies and boats to invade Cuba.