In search of a more environmentally friendly alternative to the use of chemical fertilizers, a study was conducted to evaluate the use of compost for improved crop productivity. We compared the succession of microorganisms in the compost heaps using hot bed method of composting. They contained grass clippings, sawdust, NPK fertilizer, ashes, corn cobs, bean chaff, vegetable stalks, newspaper shreds and soil arranged in layers in a round structure. Poultry dropping was the organic nitrogen source of one heap while pig waste was used for the other heap. Samples were taken weekly and analyzed using soil dilution method for isolation of moulds on potato dextrose agar medium. The qualities of composts after eight weeks were evaluated by performance and yield of tomato crops. Eleven fungal isolates were obtained in compost containing poultry dropping and nine fungal isolates were obtained from compost containing pig manure. The predominant mycoflora of poultry dropping compost at 3 weeks of composting wasFusarium pallidoroseum (23.08%) while Aspergillus fumigatus (38.96%) dominated compost containing pig waste. Fungi isolated from the composts included cellulolytic fungi like Chaetomium sp. and Phoma sp. Soil amended with both composts improved the growth and yield of tomato crop significantly. It was concluded that compost containing poultry droppings was richer and therefore encouraged higher microbial activity than compost containing pig waste. Knowledge of the microbial succession during composting and conditions required could further be employed to enhance composting.