This study aimed to evaluate the effect of the administration of aqueous extracts of Passiflora edulis and Psidium guajava leaves on the productive performance and faecal microbiology of broiler chickens from 1 to 28 days of age which were challenged with strains of coccidia (Eimerias) and an ATCC strain 13124 of Clostridium perfringens. One-day old Cobb 500 male chicks (n=100) were randomly distributed into four treatments, using five replicates and five birds per replicate. The treatments were: T1, challenged/untreated control; T2, challenged / treated control with salinomycin-nicarbazine (50g/TM) and enramycin (125g/TM); T3, challenged/treated with Passiflora edulis (60 mg/ml); T4, challenged/treated with Psidium guajava (60mg/ml). At 28 days of age, faecal samples were collected in order to determine the load of Enterobacteria and lactic acid bacteria in each treatment. The average live weight and weight gain were affected by the administration of the aqueous extracts of both plants, significantly reducing their values with respect to those of the control groups (p<0.05); whereas, no differences were observed between the treatments evaluated for the variables of food consumption, feed conversion index and percentage of mortality (p>0.05). Birds treated with the aqueous extracts of Passiflora edulis and Psidium guajava affected the Enterobacteria count, significantly reducing the number of colonies isolated in faeces of chickens at 28 days of age compared with the counts obtained in the control group challenged with Eimerias and without treatment (p<0.05), being the treatment with Passiflora edulis the most effective in reducing Enterobacteria populations than the rest of the treatments. On the other hand, both plants significantly reduced the count of lactic acid bacteria showing lower values than those found in the control groups (p<0.05).