Farmer perspectives are relevant for understanding agricultural issues and formulating policies. In this study, we conducted a cross-sectional survey on 70 Filipino farmers (i.e., 35 organic and 35 biotech) to understand farmers’ perspectives regarding coexisting farming methods. Internal response variables were tested to verify the type of decision-making processes being undertaken by biotech and organic farmers. Our results showed that a non-linear decision-making process, similar to the Stimulus–Organism–Response Model, was present for both farmer groups. The study also found that biotech farmers were more influenced by internal factors (e.g., consumer resources) than organic farmers, who rely more on external influences (e.g., culture and social interactions), in connection to their coexistence perspective. The presence of “maverick executives” within the organic farmers gives traction to the notion that coexistence can help empower farmers in choosing what farming method is most suitable to their needs. Our data can also provide insights to policymakers in terms of surveying farmer perspectives to balance farmer needs, primarily in yield and income security, with the national agricultural agenda centered on environmental conservation. Thus, farmer perspectives should be considered alongside ongoing studies and debates on coexistence.