Despite extensive research emphasizing the benefits of agroecology in Africa, its viability remains a subject of debate among policymakers, donors, and scientists. Assessing agroecological viability presents methodological challenges, which have not been systematically documented or addressed. This paper outlines key challenges encountered in evaluating agroecology across 11 case studies in Africa to guide future assessments. Seven major methodological challenges are identified: (i) defining the object of study via practices or agroecological principles, (ii) determining whether assessments should be practice-based or systemic at farm and field scales, (iii) weighing subjective farmer perspectives against “objective” evaluations of viability, (iv) choosing between qualitative and quantitative approaches, (v) conducting diachronic versus synchronic assessments, (vi) opting for a multisite approach versus a single-site study, and (vii) employing context-specific or uniform assessment methods. Findings emphasize the necessity of a multicriteria, systemic approach rooted in farmers’ perspectives, moving beyond conventional quantitative evaluation models. The study advocates for integrating both qualitative and quantitative methodologies to capture farmers’ lived experiences and insights within their farming systems, incorporating transversal and context-specific data.