Background The online delivery of yoga interventions rapidly expanded during the COVID-19 pandemic, and preliminary studies indicate that online yoga is feasible across multiple chronic conditions. However, few yoga studies provide synchronous online yoga sessions and rarely target the caregiving dyad. Online chronic disease management interventions have been evaluated across conditions, life spans, and diverse samples. However, the perceived acceptability of online yoga, including self-reported satisfaction and online delivery preferences, is underexplored among individuals with chronic conditions and their caregivers. Understanding user preferences is essential for successful and safe online yoga implementation. Objective We aimed to qualitatively examine the perceived acceptability of online yoga among individuals with chronic conditions and their caregivers who participated in an online dyadic intervention that merged yoga and self-management education to develop skills (MY-Skills) to manage persistent pain. Methods We conducted a qualitative study among 9 dyads (>18 years of age; individuals experiencing persistent moderate pain) who participated in MY-Skills online during the COVID-19 pandemic. The intervention consisted of 16 online, synchronous yoga sessions over 8 weeks for both dyad members. After the completion of the intervention, participants (N=18) participated in semistructured telephone interviews for around 20 minutes, discussing their preferences, challenges, and recommendations for improved online delivery. Interviews were analyzed by using a rapid analytic approach. Results MY-Skills participants were, on average, aged 62.7 (SD 19) years; were primarily women; were primarily White; and had a mean of 5.5 (SD 3) chronic conditions. Both participants and caregivers reported moderate pain severity scores (mean 6.02, SD 1.3) on the Brief Pain Inventory. The following three themes were identified related to online delivery: (1) participants indicated a preference for the intervention to be in person rather than online because they were distracted in the home setting, because they felt that in-person yoga would be more engaging, because the yoga therapist could physically correct positions, and because of safety concerns (eg, fear of falling); (2) participants indicated good acceptability of online MY-Skills delivery due to convenience, access, and comfort with being in their home; and (3) recommendations for improving online delivery highlighted a need for additional and accessible technical support. Conclusions Both individuals with chronic conditions and their caregivers find online yoga to be an acceptable intervention. Participants who preferred in-person yoga did so due to distractions in the home and group dynamics. Some participants preferred in-person corrections to ensure correct positioning, while others felt safe with verbal modifications in their homes. Convenience and access were the primary reasons for preferring online delivery. To improve online delivery, future yoga studies should include specific activities for fostering group engagement, enhancing safety protocols, and increasing technical support. Trial Registration ClinicalTrials.gov NCT03440320; https://clinicaltrials.gov/ct2/show/NCT03440320