This paper investigates the mediating effect of management control systems in the interaction between ambidexterity and organizational learning in Brazilian non-profit organizations. Organizational learning is addressed in the literature as an antecedent of ambidexterity, whereas the use of management control systems finds dichotomous evidence in the literature as to its effect concerning those previous constructs. This descriptive research with a quantitative approach was carried out through a survey. The research sample comprised 227 valid responses collected from the presidents of the organizations. This work reveals the positive relationship between organizational learning and ambidexterity, as well as observing that the use of management control systems tends to inhibit innovation through a mediating effect. The approach of these constructs in nonprofit environments contributes to the need for sustainability of these organizations. Findings highlight the innovative panorama of these organizations between exploitation and exploration strategies and the achievement of ambidextrous skills, also pointing out the use of management control systems, as well as the evidence of organizational learning.