<p>This paper examines the environments in which researchers operate in applied fields such as agricultural and phytosanitary science, where transdisciplinary interactions are the norm. In contrast to understandings of scientific research in terms of distinct traditions, methods and areas of research, we argue that transdisciplinary researchers operate in a highly dynamic, multi-sited and distributed research landscape, which we call multiplex research environment. As we illustrate with two case studies of crop-related research in Ghana and Italy, multiplex research environments are neither consistent nor easy to navigate, due to the presence of diverse, divergent, and dynamic commitments and demands. Individual researchers thus need to continuously negotiate tensions for knowledge to be successfully developed, while also fostering the ability to leverage unexpected exchanges or the absence of certain forms of collaborations towards fruitful forms of discovery.</p>