The Pasteur Institute of Côte d’Ivoire in its mission of surveillance and support to public health participates in the response to the COVID-19 pandemic in Côte d’Ivoire. It is involved in the diagnosis by RT-PCR of SARS-CoV-2. Through its biological resource center, which is the regional biobank of ECOWAS, the Pasteur Institute of Côte d’Ivoire keeps a priori or a posteriori nasopharyngeal samples of the COVID-19 pandemic and associated data. This study aimed to characterize the key issues driving the straw CBS^TM storage of COVID-19 pandemic nasopharyngeal specimens in Côte d’Ivoire, the key determinants of the process and the final storage protocol. Planning was used to examine the technical, economic, logistical, and political aspects of the project. The study was designed to include 100,000 samples from Abidjan, the economic capital, and the interior of the country. In the interior of the country, the samples came from COVID-19 centers in the interior cities. The biobanking process of nasopharyngeal samples in straw CBS ^TM or high security straws from a primary tube was carried out using two techniques: manual and semi-automatic. These straws are properly sealed with a guaranteed airtightness using the System of Manual Sealing (SYMS) and the semi-automated instrument (PACE) of the company CryoBioSystem (Saint Ouen sur Iton, France). The average monthly performance of the straws obtained is 1,685 for the manual technique versus 2,820 for the semi-automatic technique. This performance is in line with the objective set during the design of the study. The acquisition of the semi-automated technique (PACE) has allowed the biobank to reinforce biosafety measures concerning the handling of samples. In the event of a large-scale epidemic, the collection in a biobank requires a complete automated chain for stratification to facilitate the provision of samples to applicants and to strengthen the heritage collection.