Background Access to comprehensive exercise and rehabilitation services for people with multiple sclerosis (MS) remains a major challenge, especially in rural, low-income areas. Hence, the Tele-Exercise and Multiple Sclerosis (TEAMS) study aims to provide patient-centered, coordinated care by implementing a 12-week complementary and alternative medicine (CAM) intervention for adults with MS. However, due to the societal impact of coronavirus disease (COVID-19) in mid-March 2020, the University of Alabama at Birmingham announced a limited business model halting all nonessential research requiring on-site visits, which includes the TEAMS study. Objective In compliance with the shelter-in-place policy and quarantine guidance, a modified testing and training protocol was developed to allow participants to continue the study. Methods The modified protocol, which replaces on-site data collection and training procedures, includes a teleassessment package (computer tablet, blood pressure cuff, hand dynamometer, mini disc cone, measuring tape, an 8” step, and a large-print 8” × 11” paper with ruler metrics and wall-safe tape) and a virtual meeting platform for synchronous interactive training between the therapist and the participant. The teleassessment measures include resting blood pressure and heart rate, grip strength, Five Times Sit to Stand, Timed Up & Go, and the Berg Balance Scale. The teletraining component includes 20 sessions of synchronous training sessions of dual tasking, yoga, and Pilates exercises designed and customized for a range of functional levels. Teletraining lasts 12 weeks and participants are instructed to continue exercising for a posttraining period of 9 months. Results The protocol modifications were supported with supplemental funding (from the Patient-Centered Outcomes Research Institute) and approved by the University Institutional Review Board for Human Use. At the time nonessential research visits were halted by the university, there were 759 people enrolled and baseline tested, accounting for 92.5% of our baseline testing completion target (N=820). Specifically, 325 participants completed the 12-week intervention and follow-up testing visits, and 289 participants needed to complete either the intervention or follow-up assessments. A modified analysis plan will include sensitivity analyses to ensure the robustness of the study results in the presence of uncertainty and protocol deviations. Study results are projected to be published in 2021. Conclusions This modified remote teleassessment/teletraining protocol will impact a large number of participants with MS who would otherwise have been discontinued from the study. Trial Registration ClinicalTrials.gov NCT03117881; https://clinicaltrials.gov/ct2/show/NCT03117881 International Registered Report Identifier (IRRID) DERR1-10.2196/18415