The midfielder faces three months after fracturing his shin against Fleetwood last weekend.
Rashid Yussuff should keep his place as Moore's replacement after playing well in the 3-1 win over Bristol Rovers on Tuesday, a result which snapped a four-game losing streak at home.
The Dons are expected to start with the same XI as they did mid-week despite Mat Mitchel-King and Callum McNaughton being back in training and pressing for returns.
Dale Bennett and Pim Balkestein are both a couple of weeks away from returning to the side..
Gillingham are nursing a couple of knocks ahead of their short trip to AFC Wimbledon.
Manager Martin Allen is again giving nothing away as to the identities of those affected but did admit a few players are being assessed having suffered niggling injuries in Tuesday's 2-1 defeat at Torquay.
Full-back Joe Martin was forced off at half-time at Plainmoor, suggesting he could be one of those facing a fitness battle.
Midfielder Charlie Lee is yet to return to the fold as he looks to recover from a leg injury and it remains to be seen whether he will do so at Kingsmeadow, where the Gills will be backed by around 1,000 travelling supporters.
Defeat to the Gulls saw Gillingham lose their unbeaten away record while their second defeat of the season resulted in their lead at the top of League Two being cut to two points.