A skillful defensive midfielder, Jônatas came from Flamengo's youth team and played professionally for the club from 2002 until 2006.
He is recognizably a tactically obedient player with good technical ability which usually allows him to create attacking opportunities for his teammates and even himself.
Flamengo predicted a successful future for Jônatas if he was able to stop committing foolish fouls and complaining about referees' decisions.
In May 2007, he scored an equalizer while his team was playing with ten men against Sevilla deep into extra time to take the UEFA Cup final to penalties, but subsequently missed his kick as Sevilla went on to become only the second team after Real Madrid to retain the trophy.
In December 2006, Jônatas's father José Lourenço de Souza was kidnapped, after Robinho's family.