Atletico won just two of their seven top-flight fixtures prior to the mid-season break and found themselves in sixth position.
The only side to beat Diego Simeone's side in 14 LaLiga matches since the turn of the year is Barcelona, a run that has seen them rise to third and keep outside title chances alive.
Atletico head to the Santiago Bernabeu on Saturday on the back of five straight wins in domestic competition after beating Real Sociedad 1-0 on Tuesday, and Juanfran feels they can make things difficult for Zinedine Zidane's men.
"We went through our bad patch in November-December. Every team goes through ups and downs and it can happen to you at any point in the season," Juanfran is quoted as saying by AS.
"The poor run has made us stronger and shows that this Atleti can confront adversity. Let's hope we can keep this up until the last day.
"We haven't had time to analyse the first round of matches but it's clear that Madrid were better than us.
"But things have changed since then and now we are in a different moment, Madrid are still doing well but we have improved.
"Let's hope we can use the dynamic we are in to our advantage at the Bernabeu - it'll be difficult because they're the league leaders and they're having an incredible season.
"They are an extremely difficult team to play against; to take something from the Bernabeu we have got to be even better than we have been up until now.
"It's a big challenge for us but we have complete faith in the coach - he's leading us in the right direction to get the very best from us."