The study objective was to observe the cortisol awakening response (CAR) pattern before and after a psychosocial intervention with children from dysfunctional families who had at least one child working on the streets, and to verify factors related to it. Two hundred and eleven children between 7 and 14 years old were selected and 191 were included, 178 were re-evaluated 2 years after, of whom 113 had cortisol measures completed. Besides cortisol, they were evaluated at baseline and at end point regarding: abuse/neglect, mental health symptoms, exposure to urban violence and family environment. There was no significant difference between the CAR area under the curve (AUC) before and after the intervention. Two regression analysis models were built to evaluate factors related to the CAR before and after intervention. Before the intervention, working on the streets (vs. not) was related to a greater cortisol increase after awakening, at follow-up, having suffered physical punishment (vs. not) was related to a flattened cortisol response. The intervention was not associated with changes in the magnitude of the CAR AUC, though the CAR was associated with psychosocial stressors pre- and post-intervention. Effective interventions for children at risk that might shape a physiological cortisol response are still needed.