Coronaviruses (CoVs) are causative agents of the last three epidemics/pandemic; severe acute respiratory syndrome CoV (SARS-CoV), Middle East respiratory syndrome-CoV (MERS-CoV) and the last one SARS-CoV-2. Although meta-analysis of treatment studies against these three CoVs found no clear benefit of any spesific regimen, currently, remdesivir and favipiravir are promising potential therapies for SARS-CoV-2. On the other hand, since natural products have always played a crucial role in drug discovery and development process against various diseases, many groups in the world, are now trying to find new or repurposed natural or naturally originated drugs against viruses and CoVs. Secondary metabolites of the plants, particularly alkaloids and terpenoids have been exhibited strong antimicrobial and anticancer activities besides synthetic drugs and other natural compounds (nucleosides and nucleotides and bacterial and fungi originated ones). The first isolated secondary metabolites have been converted into important drugs since 1800's such as morphine, codeine, cocaine, and quinine have alkaloid skeleton as well as some of the recent anticancer drugs vinblastine, vincristine, taxol, etc. This review includes the last two decades of publications about natural alkaloids rather than their plant extracts which showed some promising results against CoVs. Marine organisms are also another rich source to discover new lead drugs, however they were excluded in the present review article.