Although Villa came away from the first leg of the last-16 tie with a goalless draw, they lost Ezri Konsa and Nicolo Zaniolo through suspension.
Sunday's 4-0 defeat at home to Tottenham Hotspur has only led to the desire for further alterations, Emery settling on four changes and reverting to a defensive four.
From the team that lost to Spurs, Clement Lenglet, Lucas Digne and Youri Tielemans have all dropped down to the substitutes' bench.
Diego Carlos and Alex Moreno have each been restored to the defence, while Morgan Rogers will seemingly be used on the left flank.
Moussa Diaby is also back in the side, likely starting in a central position in support of lone striker Ollie Watkins.
Meanwhile, John van't Schip has made just the only alteration to the Ajax XI that drew 2-2 with Fortuna Sittard at the weekend.
Tristan Gooijer is serving a suspension for his sending off in the first leg with Devyne Rensch coming back into the team in his place.
Van't Schip seemingly intends to stick with the same 3-4-3 formation, Jordan Henderson featuring in central midfield and Brian Brobbey leading the attack.
Aston Villa: Martinez; Cash, Carlos, Torres, Moreno; Bailey, McGinn, Luiz, Rogers; Diaby; Watkins
Subs: Olsen, Gauci, Tielemans, Digne, Lenglet, Duran, Kesler-Hayden, Iroegbunam, Kellyman
Ajax: Ramaj; Sutalo, Kaplan, Hato; Rensch, Henderson, Mannsverk, Sosa; Hlynsson, Taylor; Brobbey
Subs: Rulli, Pasveer, Gaaei, Akpom, Forbs, Medic, Rijkhoff, Van den Boomen, Vos, Fitz-Jim, Tahirovic, Godts