As of July 2011, Emanuel Villa has become one of the Top All-Time Scorers for Cruz Azul Team with 50 goals for the team. On 19 May 2012, his contract with Cruz Azul was over and both parties weren't able to end on an agreement, and on 24 May 2012 he was transferred to Pumas UNAM.
On 15 November 2012, after a poor season with Pumas he signed with Tigres UANL. On 5 January 2013, Villa made his official league debut with Tigres against Chiapas scoring a hat trick in the Estadio Universitario. On 19 January 2013, Villa scored the goal for the victory of 1–0 of Tigres over Atlas de Guadalajara. Villa scored one goal and gave an assist to Danilinho to the second goal in the victory of 2–0 of Tigres over Queretaro F.C. in the Estadio Corregidora on 26 January 2013. On 10 February 2013, Villa scored one goal against Toluca for the victory of 4–1, in the Estadio Nemesio Díez. On 23 February 2013, Villa scored for the first time on his career against his former team Cruz Azul. He scored the two goals of the victory of 2–1, at the Estadio Azul. On 28 February 2013, while training, Villa suffered from a strain on his left calf. He missed five games. On 14 April 2013, he scored once more against a former team, this time to Pumas UNAM at the Estadio Olímpico Universitario in the defeat of Tigres by 2-1. On 6 July 2013, Villa scored one goal for the victory of 5-1 against San Antonio Scorpions in a friendly game at the Toyota Field. On 18 September 2013, he scored a goal against Club Santos Laguna in the Copa MX at the Estadio Universitario for the 3-0 victory of Tigres. On 2 October 2013, Villa scored a goal against archrival C.F. Monterrey for the 2-2 draw in the Copa MX quarterfinals played at the Estadio Tecnológico. Due to past physical issues and looking for a full recovery, Villa did not play with Tigres the Clausura 2014 tournament. On mid-May, 2014, Villa reported as ready for the Apertura 2014 tournament. He scored a goal against Club León on the victory of Tigres by 4-2 at the Estadio Universitario on 26 July 2014, on the second game of the league regular season. Villa participated scoring the third goal of a 5-1 victory over Monarcas Morelia at the Estadio Morelos, heading in a cross from Darío Burbano on a league game on 22 August 2014.