Introduction. This research analyzed the internal control systems in the agricultural economic units of the municipalities of Soyaniquilpan and Jilotepec, given that these units, mostly composed of informal producers, frequently lacked clearly defined processes, which hindered staff training and affected the expected income from agricultural activity. Objective. The study aimed to evaluate the efficiency of the internal control procedures implemented and to determine their relationship with business profitability. To this end, a univariate descriptive study was conducted using a five-point Likert-scale survey applied to 30 participants, whose data were processed with SPSS software. Methodology. The study was conducted using a quantitative approach, with a non-experimental, cross-sectional design, and a descriptive scope. Data was collected through a survey administered to 53 businesses across various economic sectors in the Morona canton, using a structured questionnaire with a Likert scale, and the data were analyzed using IBM SPSS Statistics software. Results. The results revealed significant weaknesses in the internal control system, particularly in the manual control, periodic evaluations, and supervision, while profitability indicators showed a moderately positive perception. Conclusion. It was concluded that a gap existed between the fragility of internal controls and perceived profitability, and that the agricultural units sustained their financial viability through external factors, such as favorable weather conditions and access to support programs, rather than through robust formal controls. These findings highlighted the need to strengthen internal control systems to consolidate the sustainability of the agricultural sector in the region studied. General Area of Study: Administration. Specific area of study: Administration Type of study: Original article.