The Ministry of Ayush (MoA), either independently or in collaboration, has diligently endeavoured to ascertain the significance of India's Ayush system in mitigating and managing COVID-19 pandemics since its inception. Despite the various constraints posed by limited resources and other impediments, a substantial amount of research has been undertaken in the Ayush arena, as evidenced by the considerable number of clinical trials registered in the Clinical Trial Registry of India (CTRI) and further on the several medical databases. To summarise the clinical trials of Ayush interventions against COVID-19, a living systematic review and meta-analysis were conducted at ITRA, Jamnagar in collaboration with South-East Asia Regional Office of World Health Organisation (WHO SEARO), New Delhi. During the course of this process, several research gaps and challenges have been observed. Researchers observed that many studies lacked in quality owning to design, execution or analysis level. There is a huge need for the upliftment of the research environment in the Ayush system of Medicines. This article has highlighted the gaps in the scientific literature, its impact on evidence quality and the feasible and practical solutions to rectify those. Continuous capacity-building to human resources, incorporation of a whole system approach in research design without breaking integrity and validity and adherence to standard international guidelines in protocol designing and reporting are a few of the propositions for future endeavours. The analysis of these issues is crucial for the prospective development of research in the field of traditional medicine.