The Serie A giants have had an inauspicious Serie A campaign, winning just four of their 15 league fixtures so far.
Massimiliano Allegri's charges also had to sweat on their progression from Champions League Group H, as Riccardo Montolivo's first-half sending off ensured they had to hold on for much of their game against Ajax to secure the point they needed to progress last week.
Gandini recognised the attacking threat posed by Diego Simeone's side, who sit second in La Liga, but believes a full strength Milan side can progress to the quarter-finals.
"Atletico are a very strong side who play great football under Simeone," he said.
"They are very strong in attack but it could be even worse for us considering the sides we could have picked.
"We will have to see how both sides will be in two months. We have had several injuries in the first part of the season, hopefully we will have a fully fit squad in February."
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