At the end of December 2010, there was information that Cristaldo could move to Kharkiv "Metalist". On January 8, 2011, Jonathan arrived in Kharkiv together with Sebastian Blanco to sign a contract with Metalist and ended up signing a five-year contract with the club. Cristaldo took number 21.

Honatan Cristaldo during performances for "Metalist". August 18, 2011

In the Kharkiv club, he made his debut in official matches in February 2011 in the Europa League, where "Metalist" suffered a crushing defeat with the German "Bayer" 0:6 in the sum of two matches, and Khonatan played in both matches. In the championship of Ukraine, Cristaldo could not score for a long time, but on May 8, 2011, in the 28th round, he immediately scored a hat-trick against Volyn, and in the last round he scored a double against Obolon, officially formalizing the championship's bronze medals.

In the next two seasons, Cristaldo, along with Marko Dević, was the team's main forward, regularly scoring goals, including in European Cups. Moreover, in the 2012/13 season, Khonatan's 9 goals helped "Metalist" to win the championship's silver medals for the first time in history.

He also started the 2013/14 season in Kharkiv, scoring three goals in the first seven matches of the championship, but due to Devych's excellent form, as well as the lack of a Ukrainian passport, he could not be a full-fledged striker of the club, coming mostly to substitutes.