 His own tomb is there, as well as that of his mother, Aldonza de la Vega, and that of his wife.His firstborn and heir was Lorenzo Manuel de Villena y Rojas, commander of the Order of Alcántara and senior butler to Charles V. His younger sons were Juan, bishop of Sigüenza (r. 1574–1579), Pedro, Lorenzo and Rodrigo.Juan Manuel appears as a character in a number of Spanish historical films, including
"Juana la Loca" (2001), played by Chema de Miguel,
"Isabel" (2014), played by Jacobo Dicenta, 
and "La corona partida" (2016), again played by Jacobo Dicenta.