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Ben White, who also missed last week’s 2-2 draw with Palace, trained as well and is on the bench in what is a further boost for Mikel Arteta.
Merino has been starring up front for Arsenal since February, but he is playing in midfield on Tuesday.
Thomas Partey is suspended whilst Arteta is also without fellow defensive midfielder, Jorginho, due to a rib injury and defender Riccardo Calafiori.
“We know that we lost Thomas unfortunately very late in the game against Real Madrid,” Arteta said in the pre-match press conference.
“Ben and Mikel, they were able to train [on Monday]. Let’s see if they are able to start tomorrow, and Ricky is still not fit.”
Partey’s absence means Declan Rice is likely to be tasked with playing at the base of midfield, instead of his usual No8 role.
Merino drops into the midfield alongside Rice and captain Martin Odegaard, with Leandro Trossard leading the line.
Bukayo Saka and Gabriel Martinelli flank him on either wing, with the latter a second-half substitute in last week’s draw with Palace.
At the back, Arteta sticks with the defence that kept Real Madrid quiet in the last round. It means another start for Jakub Kiwior alongside William Saliba in the heart of defence.
Arsenal XI: Raya; Timber, Saliba, Kiwior, Lewis-Skelly; Odegaard, Rice, Merino; Saka, Trossard, Martinelli
Subs: Neto, Setford, White, Tierney, Zinchenko, Henry-Francis, Nwaneri, Butler-Oyedeji, Kabia, Sterling
Injured: Calafiori (knee), Gabriel (hamstring), Havertz (hamstring), Jesus (knee), Jorginho (ribs), Tomiyasu (knee)
Time and date: 8pm BST on Tuesday April 29, 2025
How to watch: Amazon Prime
Referee: Slavko Vincic (Slovenia)
Arsenal squad from: Neto, Raya, Setford; Kacurri, Kiwior, Lewis-Skelly, Saliba, Tierney, Timber, Zinchenko; Merino, Nwaneri, Odegaard, Rice; Martinelli, Saka, Sterling and Trossard