The right-back, who has started seven LaLiga games and three UEFA Champions League fixtures this term, sustained a calf injury in Thursday's training session.
Santiago Arias is likely to retain his place in Juanfran's absence, but manager Diego Simeone has a selection headache for the visit of the league leader.
Captain Diego Godin is expected to be unavailable after he damaged his left hamstring in Atletico's last match – an injury that did not prevent the centre-back from netting a dramatic late winner.
Fellow Uruguay international Jose Gimenez has been sidelined with a similar complaint and is in a race to be fit alongside another defender Lucas Hernandez (adductor).
Barcelona top the table heading to the Wanda Metropolitano but they are only a point clear of Atletico, who have won four of their past five games in all competitions.
After hosting the defending champion, Atletico are at home to Monaco in Group A of the UEFA Champions League on Thursday (AEDT), needing a win to secure qualification.