The Inquiry Cycle represents an integrated methodology for field investigations under continuous development in Latin America since 1994. The investigator first formulates the research question following an explicit sequence of observation, conceptual framework and site-specific concern. The research question must comply with five criteria that directly frame the design of the field study in itself and later the discussion of results (reflection). In particular, the question specifies the design factors and the response units or experimental units, and the response variables to be recorded in each response unit. These elements lead to a detailed, 17-step process of study design. Similarly, the reflection phase follows an ordered, cautious, and creative review of the results once obtained, examines all possible causal factors, and cautiously but creatively suggests possible extrapolations to other contexts and scales. All steps of the Inquiry Cycle as a research methodology also serve as the template for writing a complete and objective thesis or publication. For research involving forest management, wildlife management, agroecology, conservation biology, or another aspect of applied field biology, the Inquiry Cycle adds a fourth explicit step (application). It is now the Applied Inquiry Cycle, codifying the process of adaptive management. Today the two Cycles provide the Chilean Long-term Socio-ecological Research Network with a research protocol for applied as well as basic studies.