Born in Ermesinde, Porto District, Josué joined FC Porto's youth system at the age of nine. He spent his first two seasons as a senior on loan, both in Portugal and abroad, representing successively S.C. Covilhã, F.C. Penafiel and VVV-Venlo. In summer 2011, Josué was released by Porto with only two official appearances to his credit, both in the Taça da Liga, and signed with F.C. Paços de Ferreira. He made his Primeira Liga debut on 17 September, playing the full 90 minutes in a 0–1 away loss against C.D. Nacional; in his second year he contributed with 23 league appearances – 18 starts – as the club finished a best-ever third and qualified to the UEFA Champions League, and was chosen as Best Young Player in the competition in the process.
Return to Porto
Josué agreed on a return to former side Porto on 29 May 2013, penning a four-year contract and moving alongside manager Paulo Fonseca. On 10 August he won his first club honour, coming on as a substitute in a 3–0 win over Vitória de Guimarães in the Supertaça Cândido de Oliveira, and scored his first goal for his new team a week later starting and netting through a penalty kick in a 3–1 win at Vitória de Setúbal. Deemed surplus to requirements at Porto as practically all Portuguese players, Josué then spent 18 months on loan at Bursaspor. He made his Süper Lig debut on 30 August 2014, coming on as a late substitute in a 0–2 home loss against Galatasaray SK, and helped the team to the final of the Turkish Cup, notably contributing with a brace to a 3–2 group win at Samsunspor on 24 December 2014. On 26 January 2016, he returned to his homeland and was loaned to S.C. Braga for the rest of the campaign, netting against his parent club in the decisive match of the Taça de Portugal that was won in a penalty shootout for their first such title in half a century. On 23 August 2016, Josué returned to Turkey, joining Galatasaray on a season-long loan. He scored his first goal for the Istanbul-based team on 25 December, closing a 5–1 home win over Alanyaspor six minutes after replacing Eren Derdiyok.
Later career
Josué left Porto in August 2017, signing a two-year contract at Osmanlıspor again in Turkey's top flight. He was released in December, and resumed his career the following July with a deal of the same length at Akhisarspor. His side finished runners-up in the Turkish Cup to former club Galatasaray, with him scoring in both legs of a 5–2 aggregate defeat of Kasımpaşa S.K. in the quarter-finals. Nonetheless, Akhisarspor were relegated, and Josué severed his ties to the organisation in June 2019. In September he signed for Hapoel Be'er Sheva F.C. of the Israeli Premier League for two years, joining compatriot Miguel Vítor.