ABSTRACT The implementation of a Good Agricultural Practices (GAP) program, seeks mainly to reduce the risks associated with agricultural production, as a primary component of the complex agro-food chain, although in principle the GAP were directed toward the prevention of hazards associated with hygiene and food safety, its scope has grown and now includes topics related to environmental protection, welfare and safety of workers and traceability, as constituent elements of a quality management system. The current incidence of quality in the scope of food, calls upon those responsible of organizations of the industry to implement a protocol that allows them to ensure that their products are tailored to the exacting standards of hygiene and quality, which facilitates access to the high valued specialized markets. The main failures in a GAP program are due to the uncertainty that occurs in the implementation phase of the protocol, as a result of the insufficient attention paid to those aspects where the results largely have influence on the success of quality management in an organization, commonly referred to as Critical Factors. This work developed in the form of a "Ph.D. Thesis", comprises two main sections, the first section is performed to identify the critical factors to implement a GAP program on coffee and fruits farmers in the department of Huila in Colombia, using a Principal Component Analysis (PCA) on the results of the implementation of two assessment tools with defined structure: the instrument Starbucks C.A.F.E. practices – small scale coffee growers - for coffee producers and the instrument EUREPGAP V2.1 Oct.2004 / Checklist for fruits and vegetables, as applied to fruit producers. The second part of the study was seen as the solution to a complex decision problem, in order to establish the priorities of the factors identified in the previous section, on the implementation of the protocol of good agricultural practices, was resolved through the use of a Multiple Criteria Decision-Making (MCDM) method, specifically using a Analytic Hierarchy Process (AHP), and also it was defined the most suitable order to implement alternative solutions that will overcome the barriers imposed by the critical factors. The multivariate statistical methods and, specifically, the exploratory factor analysis, preceded by a descriptive analysis, allowed us to identified six critical factors: infrastructure, activities of the established production process, making and data reporting, environmental awareness, welfare and safety of workers, and quality control; for its part, the solution to the complex decision problem, determined that the most influential barrier to implementing a GAP program, is the infrastructure factor, and that the other critical factors reach a significant level of involvement, warning us about the risks of disregarding any of the identified critical factors; additionally, through the hierarchical analysis of alternative solutions, we recommend that before making any investment in infrastructure a training program, on those areas which were found major weaknesses, must be implemented.