Aguilar returned to Udinese in January 2006, after having never played for Ascoli, but received few playing opportunities in the following months (two league matches and the UEFA Cup 0–1 loss at RC Lens, all incomplete).

For the following three years, Aguilar was also loaned, always in the Spanish second division. He started out in January 2007 at Xerez CD, where he remained until the end of the 2007–08 campaign, always as first choice.

In 2008–09, Aguilar represented Hércules CF, being a permanent fixture as the Alicante side fell three points short of a return to La Liga. On 24 July 2009 he was again loaned, now to Real Zaragoza, which in turn promoted to the top flight; he made his debut in the competition on 29 August, starting and playing 71 minutes in a 1–0 home win against CD Tenerife, and scored all his four league goals during the first two months of competition.

Aguilar was released by Udinese in July 2010, immediately signing a four-year contract with former club Hércules, returned to the top division after an absence of 13 years. He appeared in 34 scoreless games during the season, which ended in relegation.

On 22 August 2013, Aguilar agreed to a three-year deal with Toulouse FC. His maiden appearance in Ligue 1 occurred nine days later, putting on an average performance and being booked in a 1–2 away loss to SC Bastia.

On 12 June 2016, after 11 years playing in Europe, Aguilar returned to his country and Deportivo Cali, signing a three-year contract. He scored his first goal for the team on 29 July, in the 2–1 victory against América de Cali for the Copa Colombia.

On 27 August 2018, Aguilar joined Major League Soccer side FC Dallas. At the end of the season, he was released.

Aged 33, Aguilar returned to his country in December 2018, agreeing to a deal at Unión Magdalena for the upcoming season. On 18 February 2020, he announced his retirement.