In this article, we explore elements that highlight the interdependent nature of demands for knowledge production and decision-making related to the appearance of emerging diseases. To this end, we refer to scientific production and current contextual evidence to verify situations mainly related to the Brazilian Amazon, which suffers systematic disturbances and is characterized as a possible source of pathogenic microorganisms. With the acceleration of the Anthropocene's environmental changes, socio-ecological instabilities and the possibility of the emergence of infectious diseases merge into a background of a ´twin insurgency´. Furthermore, there is a tendency to impose economic hegemony in the current Brazilian context, corroborating discourses and pressures to a scientific simplification and denial. With this, we assert that developmental sectoral actions and monoculture of knowledge characterize an agenda of omission, that is, a process of decision making that indirectly reinforces ecological degradation and carelessness in the face of the possibility of the emergence and spreading of new diseases, such as COVID-19. Tackling the socio-ecological complexity inherent in the risk of the emergence of infectious diseases requires robust co-construction of scientific knowledge, eco-social approaches, and corresponding governance and sophisticated decision-making arrangements.