Atletico fans had to endure a disappointing campaign as the side finished seventh in La Liga, and were hit with further blows over the summer as star attacking duo Sergio Aguero and Diego Forlan departed for Manchester City and Inter Milan respectively.
However, the club have brought in capable replacements in the form of Radamel Falcao, Diego and Arda Turan, and speaking ahead of their match at the Mestalla this Saturday, Emery admits he is concerned with the threat Atletico will pose.
"We are already thinking about the match against Atletico, a team who let go of their two biggest names but who have replaced them with important players," Emery told EFE.
"Atletico are still a very dangerous team and Saturday's match will be the first of an intense series of contests for which we will be needing the entire squad."
Following the encounter with Atletico, Valencia will take on Sporting Gijon, Barcelona and Sevilla in their next three league matches, along with UEFA Champions League ties against Genk and Chelsea.
And while Valencia were just one of six teams that managed a win in their opening La Liga match of the season, a last-gasp 4-3 victory over Racing Santander, Emery knows his side will have to improve in defence if they are hoping for positive results over the next month.
"We have to play harder in defence and we are working on that."
Atletico kicked off their season with a 0-0 draw against Osasuna.