The handling practices of cow dung were examined in two (2003 and 2004) seasons to determine their effects on the Calcium and Magnesium content and the microbial population in Northern Nigeria. The experiment consisted of four treatments (surface heaped uncovered, surface heaped covered and pit covered) and a control (untreated). The results revealed that, subjecting the cow dung to different handling practices significantly (P < 0.05) increased values of Calcium and Magnesium and the total bacterial and fungal populations, compared to the control. At termination of composting of the cow dung, the heaped uncovered method gave significantly (P < 0.05) higher values of Calcium and Magnesium in the two years, while after field storage, it was the heaped covered method that gave significantly (P < 0.05) higher values of the Calcium and Magnesium for the two years. In each case where the nutrient content (Ca and Mg) was high, the microbial population of bacteria and fungi was also high. It is therefore concluded that, the high Calcium and Magnesium content of cow dung was directly related to the high population of bacteria and fungi. It is therefore recommended based on this work, that cow dung should be used immediately after composting using the heaped uncovered method, while the heaped covered method is recommended if it is to be used after field storage.