COVID-19 pandemic movement restrictions as part of the control measures put in place by countries in Sub-Saharan Africa (SSA) has implications on many sectors which include very high costs of importing materials owing to high exchange rates as well as non- availability of microbial cultures for food/ industrial productions, medical/academic research and applications because of fear of new microbial infections and bio-terrorism. Overcoming these challenges in SSA requires developing better policies and packages to confront the challenges by way of rebooting their strategies and policies for sustainable economic growth through reawakening the potentials they have. The maintenance and production of reliable pure microbial cultures with desirable quality is a key operation and is the first significant stage in the success of fungal applications in any scientific venture where they are used. For many years the process of freeze-drying (lyophilisation) has been employed primarily with the purpose of preserving living materials, including microorganisms, for extended periods of time; this is possible because, upon dehydration, substances no longer change as a consequence of the usual turnover of metabolic reactions characteristic of the living condition. This study assessed lyophilization (freeze drying) of some indigenous filamentous fungal cultures (Spores) using skim milk and honey (supports being maize and cassava flours) as the protectants and then critically compared the two protective media for the preservation of active filamentous fungi spores for the first time, and from the data obtained, their applications were optimised. Some fungal isolates(Aspergillus sp., Mucor sp., Penicillum sp., Fusarium sp., Rhizopus sp., Cladosporium sp. Alternaria sp. and Geotricum sp.) previously purified and identified were obtained from the Products Development Unit, National Biotechnology Development Agency, Abuja, Nigeria and were re-validated where their viability and purity were confirmed. The samples were Freeze Dried in the respective medium and monitored immediately after. After the freeze‐drying, the residual water contents were between 0.20-0.32%, 0.39-0.49% and 0.33-0.41%, respectively, with skim milk, Honey with Cassava Starch and honey with Maize Starch. The driedspore viabilities were between 96% (Aspergillus spores in Reconstituted Skim Milk) and 21% (Geotricum spores in Honey with Cassava Starch. Among the protective agents used, skim milk was found to be the best protectant.Each fungal isolate was considered viable if the rate of growth present was the same as that of the original culture and if the morphology of the colony matched the fungal identification documented for each species. All lyophilized fungal species were found viable from both type of lyophilized materials, skim milk and honey and showed the initial colony characteristics and growth rates.