The forward suffered a nasty tackle in the first half of PSG's Coupe de France final victory over Saint-Etienne on Friday, and took part in the trophy celebrations after the 1-0 win while on crutches.
It now seems very likely he will not be fit in time to face the Serie A side, with PSG saying Mbappe will be out for at least three weeks.
A PSG statement on the club website said: "As announced after the final of the Coupe de France against Saint-Etienne, Kylian Mbappe was examined on Monday in order to know the severity of his right ankle injury.
"The examination performed today confirms a sprained ankle with external ligament injury. Following this, the recovery time is estimated at around three weeks."
This means Mbappe wouldn't be fit in time to face Atalanta on August 12, although he could return for the semi-finals and final of the Champions League tournament held in Lisbon, should PSG make it that far.
The latter stages of the leading European club cup competition are taking place in the Portuguese capital over a series of one-off games next month, rather than the usual two-legged home and away affairs, after they were rescheduled due to the coronavirus pandemic.
The highly condensed nature of the competition means PSG will be sweating on the fitness of one of their biggest stars as they attempt to win the Champions League for the first time in their history.
The saving grace for PSG is that the France international has avoided serious ligament damage or any broken bones following Loic Perrin’s tackle on Mbappe, which earned the Saint-Etienne captain a straight red card.
They also have the Coupe de la Ligue final against Lyon to negotiate on July 31, as they look to complete a domestic treble before refocusing on August’s revamped Champions League.
While Thomas Tuchel's side will still be considered heavy favourites by many going into the clash with Atalanta, Gian Piero Gasperini’s side have scored 96 goals in 36 Serie A games this season so cannot be underestimated.
Tuchel will still have considerable attacking talent to choose from if Mbappe is unavailable but with Edinson Cavani having already departed after the end of his contract, it would be a significant blow.
Mbappe has scored 30 goals and registered 18 assists in 34 appearances for PSG this season. That includes five goals and five assists in seven games in the Champions League.