Low fruits consumption contributes to micronutrient deficiency particularly in populations with low consumption of animal source foods. This study was carried out to assess the fruits availability and consumption; and to determine factors influencing their consumption; fruits storage practices and their effects in influencing the nutritional and microbial quality of fruits. Information about fruits availability, consumption and storage practices was collected by using semi structured questionnaire, and food frequency questionnaire. Laboratory analysis of baobab fruits was carried out to determine moisture content, vitamin C, total carotenoids, yeast and mould and total bacteria count. Result on fruits consumption show that, majority of households consumed fruits rarely, weekly, monthly and while few of them consumed fruits daily. The average daily fruit consumption was 47.1grams/day and 58.7grams/day for mothers and children respectively which is far below the minimum amount of 400grams/day recommended by WHO/FAO. Factors that significantly affected fruits consumption were household’s monthly income, household size and household sex headship. Results on fruits storage show that baobab fruits were stored by 88.4% households as they are not perishable compared to other fruits. Baobab storage practices identified in the study area were sack (polystyrene) storage (77.4%), plastic storage (3.3), in pot storage (0.33%), basket storage (0.66%) and shelled fruits storage practices (18.4%). These storage practices when singly or combined with other factors such as storage time and location influenced the nutritional and microbial quality of baobab fruits. Fruits stored in plastic had more vitamin C (167.82mg/100g) compared to those stored in shells (160.64mg/100g) and those in sacks (136.4g/100g). Total carotenoids were found more in samples stored in shells (2.28g/100g) than those in plastic and sacks. Highest moisture content was recorded in samples stored in sacks compared to those in plastic and shell. High microbial content of total bacterial counts and mould and yeast was found in sack stored samples than in plastic and shelled samples. Moisture content, vitamin C and total carotenoids decreased after six months of storage. The mould and yeast and total bacteria count increased after six months of storage. Interactive effect of storage practices and time showed that, sack storage caused a reduction in nutritional quality of fruits while led to increased microbial contamination of samples after six months of storage. Interactive effect of storage time, practice and location showed that, samples from Chinoje stored in sacks taken after six months of storage had a significantly low vitamin C compared to other samples. Also samples taken after six months of storage, from Chinoje, stored in sacks, had the highest number of microorganisms. It is concluded that sack storage of baobab fruits is not good since it did not retain nutrients during storage compared to plastic and shell storage. Also it resulted to more microbial contamination of fruits compared to plastic and shell storage.