Malaga confirmed the setback in a statement on their official website on Tuesday.
Juanmi, who has scored in three of his last four appearances, will undergo surgery next Monday in order to correct the injury.
The 21-year-old is therefore certain to miss this weekend's home game against Liga leaders Real Madrid.
Juanmi's injury comes at a particularly inconvenient time given his recent goalscoring form.
He was on target against Rayo Vallecano, Real Sociedad and Eibar prior to the recent international break as Javi Gracia's men extended their winning streak to five matches.
However, Juanmi failed to score when Malaga went down 3-1 to reigning champions Atletico Madrid on Saturday.