Background As the COVID-19 crisis endures and the virus continues to spread globally, the need for collecting epidemiological data and patient information also grows exponentially. The race against the clock to find a cure and a vaccine to the disease means researchers require storage of increasingly large and diverse types of information; for doctors following patients, recording symptoms and reactions to treatments, the need for storage flexibility is only surpassed by the necessity of storage security. The volume, variety, and variability of COVID-19 patient data requires storage in NoSQL database management systems (DBMSs). But with a multitude of existing NoSQL DBMSs, there is no straightforward way for institutions to select the most appropriate. And more importantly, they suffer from security flaws that would render them inappropriate for the storage of confidential patient data. Motivation This paper develops an innovative solution to remedy the aforementioned shortcomings. COVID-19 patients, as well as medical professionals, could be subjected to privacy-related risks, from abuse of their data to community bullying regarding their medical condition. Thus, in addition to being appropriately stored and analyzed, their data must imperatively be highly protected against misuse. Methods This paper begins by explaining the five most popular categories of NoSQL databases. It also introduces the most popular NoSQL DBMS types related to each one of them. Moreover, this paper presents a comparative study of the different types of NoSQL DBMS, according to their strengths and weaknesses. This paper then introduces an algorithm that would assist hospitals, and medical and scientific authorities to choose the most appropriate type for storing patients’ information. This paper subsequently presents a set of functions, based on web services, offering a set of endpoints that include authentication, authorization, auditing, and encryption of information. These functions are powerful and effective, making them appropriate to store all the sensitive data related to patients. Results and Contributions This paper presents an algorithm to select the most convenient NoSQL DBMS for COVID-19 patients, medical staff, and organizations data. In addition, the paper proposes innovative security solutions that eliminate the barriers to utilizing NoSQL DBMSs to store patients’ data. The proposed solutions resolve several security problems including authentication, authorization, auditing, and encryption. After implementing these security solutions, the use of NoSQL DBMSs will become a much more appropriate, safer, and affordable solution to storing and analyzing patients’ data, which would contribute greatly to the medical and research effort against COVID-19. This solution can be implemented for all types of NoSQL DBMSs; implementing it would result in highly securing patients’ data, and protecting them from any downsides related to data leakage.