In school-based research, isolating the potential effects of a single variable while attempting to maintain typical classroom routines is always a challenge. Unfortunately, the challenges and methodological approaches to overcoming them are often only shallowly reported, perhaps due to word limits or assumptions that those details are irrelevant to the findings. Thus, future research is unnecessarily impeded, destined to repeat the same mistakes. In this article, we reflect on the design and methodological strengths of our study of nature-based instruction (NBI) and how some strengths also created challenges with implications for interpreting the findings of our study (published in a companion paper, Faber Taylor, Butts-Wilmsmeyer, and Jordan 2022). In that study, we attempted to isolate the potential effects of NBI compared to classroom-based instruction on science learning and to test for potential mechanisms and moderating variables. We share insights in hopes of supporting others' research design and nature-based educational practice.