On 1 January 2013, Msakni became a player of Qatari club Lekhwiya SC for a period of four and a half years; the total amount of the transfer was 23 million dinars (€11.5 million), a record for an African player.
On 10 February, he scored his first goal in the 28th minute, with his team winning 4–0 against Al-Wakrah SC. On 26 February, Msakni proved decisive in the AFC Champions League with a free-kick in the 33rd minute, allowing his team to win 2–1. In March 2013, Msakni was reportedly coveted by four English clubs: Newcastle United, Arsenal, Everton and Tottenham. This growing interest pushed the Qatari club leaders to review the player's release clause by increasing his price. On 4 May, he won the 2013 Qatar Crown Prince Cup against the Al Sadd after scoring his team's third goal in a 3–2 win.