In 2006, Sebastian was inducted into the Billboard Latin Music Hall of Fame for his prolific songwriting and musical arrangements. Sebastian was awarded Songwriter of the Year three times by ASCAP and received the Golden Note Award in 2007 in recognition of his songwriting career.
Sebastian had eight children from five different women. Their names are José Manuel Figueroa (who is also a singer and composer), Juan Sebastián Figueroa González, Trigo de Jesús Figueroa González (first three children with Teresa González, his first wife), Zarelea Figueroa Ocampo (who is also a singer and composer), Marcos Julián Figueroa Fernández (son of Maribel Guardia, who's a singer and has a son with Imelda Tuñon), Joana Marcelia Figueroa Espín, Juliana Joeri Figueroa Alonso and D'Yave Figueroa Espín. His third oldest son, Trigo was shot in the back of the head after one of Joan Sebastian's concerts in Mission, Texas on August 27, 2006. Trigo had been trying to control the crowd after the show. He was transported to McAllen Medical Center where he was pronounced dead.