Background Extensive evidence supports a link between aerobic exercise and cognitive improvements in aging adults. A major limitation with existing research is the high variability in cognitive response to exercise. Our incomplete understanding of the mechanisms that influence this variability and the low adherence to exercise are critical knowledge gaps and major barriers for the systematic implementation of exercise for promoting cognitive health in aging. Objective We aimed to provide an in-person and remotely delivered intervention study protocol with the main goal of informing the knowledge gap on the mechanistic action of exercise on the brain by characterizing important mechanisms of neuroplasticity, cardiorespiratory fitness response, and genetics proposed to underlie cognitive response to exercise. Methods This is an open-label, 2-month, interventional study protocol in neurologically healthy sedentary adults. This study was delivered fully in-person and in remote options. Participants underwent a total of 30 sessions, including the screening session, 3 pretest (baseline) assessments, 24 moderate-to-vigorous aerobic exercise sessions, and 3 posttest assessments. We recruited participants aged 55 years and above, sedentary, and cognitively healthy. Primary outcomes were neuroplasticity, cognitive function, and cardiorespiratory fitness. Secondary outcomes included genetic factors, endothelium function, functional mobility and postural control, exercise questionnaires, depression, and sleep. We also explored study feasibility, exercise adherence, technology adaptability, and compliance of both in-person and remote protocols. Results The recruitment phase and data collection of this study have concluded. Results are expected to be published by the end of 2021 or in early 2022. Conclusions The data generated in these studies will introduce tangible parameters to guide the development of personalized exercise prescription models for maximal cognitive benefit in aging adults. Successful completion of the specific aims will enable researchers to acquire the appropriate expertise to design and conduct studies by testing personalized exercise interventions in person and remotely delivered, likely to be more effective at promoting cognitive health in aging adults. Trial Registration ClinicalTrials.gov NCT03804528; http://clinicaltrials.gov/ct2/show/NCT03804528 International Registered Report Identifier (IRRID) RR1-10.2196/33589