Lindor attended Montverde Academy in Montverde, Florida. The school's baseball facility was named after him in 2013. He was named to the USA Today All-USA high school baseball team. The Indians drafted Lindor in the first round (eighth overall) of the 2011 MLB draft. He had full-ride scholarship offer in place with the Florida State Seminoles baseball team, but chose to sign with the Indians for $2.9 million in August. In September, Lindor was drafted by the Indios de Mayagüez in the second round of the Liga de Béisbol Profesional Roberto Clemente's (LBPRC) first year draft. However, he has been unable to play there due to Cleveland's intervention. On May 7, 2014, the Indios de Mayagüez traded Lindor's LBPRC player rights to the Gigantes de Carolina in exchange for Carlos Correa. However, only two weeks later the Cangrejeros de Santurce signed him by exploiting a legal loophole declaring that any player that has not been officially contracted within three years after being drafted is considered a free agent.
Prior to the 2013 season, Baseball America ranked him as the Indians top prospect. Lindor started the 2013 season with the Carolina Mudcats of the Class A-Advanced Carolina League. He was promoted to the Akron Aeros of the Class AA Eastern League on July 15, 2013. Between the two levels, Lindor batted .303 with two home runs, 34 RBIs, 31 extra-base hits, and 25 stolen bases in 104 games.