In 2011 Cafú signed for Boavista, but appeared in only one match for the club during his spell (a 1–1 Campeonato Carioca home draw against América-RJ on 19 January).

Cafú appeared in 32 matches for Macaca, scoring six goals (his first being on 31 May, the winner against Boa Esporte), as his side returned to Série A at first attempt.

On 27 July 2015, Jonathan Cafú moved abroad to Europe to join Bulgarian side Ludogorets Razgrad[4] for a record club fee of €2.2 million.

[5] On 8 August, Cafú played full 90 minutes for Ludogorets's reserve team in a league fixture against Vereya of the B Group.

His good performances continued as he scored a goal and provided an assist to Claudiu Keșerü to give his team a 2–0 lead in the home match against Arsenal, which Ludogorets eventually lost by 2–3.