The COVID-19 pandemic had an immense impact on the world, affecting millions of people and prompting medical professionals to work tirelessly to save lives. In addition to conventional medicine, ancient Indian practices such as Yoga, Ayurveda, and Homeopathy played a significant role in managing the disease. This systematic review evaluates the effects of Yoga and other alternative therapies on COVID-19 complications. Various electronic bibliographic databases, including Medline (PubMed), Cochrane Library, AYUSH research portal, WHO COVID-19 Research Database, and Google Scholar, were searched up until December 31, 2022. The methodological quality of the studies was assessed using the Physiotherapy Evidence Database scale. The screening process of the initial 2034 identified articles yielded 15 randomized controlled trials, which incorporated Yoga (n = 5), Ayurveda (n = 7), Homeopathy (n = 2), and Yoga with Ayurveda (n = 1). All the studies showed significant effects of Yoga and other alternative therapies on time taken for recovery, inflammatory markers, or questionnaire scores in COVID-19-infected individuals or survivors. The findings of this systematic review indicate that Yoga, Ayurveda, and Homeopathy, alongside conventional medicine, are effective in managing complications related to COVID-19. However, to improve the quality of evidence, further studies with larger sample sizes and multi-level blinding are necessary.