The aim of this study is to investigate the prevailing physico-chemical changes and microbial structure during composting of agricultural wastes. Two kinds of crop residues (rice straw and cotton stalks) were selected with cattle dung to make nine mixtures. Some of these mixtures were mixed with natural amendments to investigate their influences on composting process and the end product. The composting process was allowed to continue up to 12 weeks. Results showed that all physical, chemical and biological properties of mixtures were strongly influenced by the type of raw wastes and natural additives. Where, pH and electrical conductivity (EC) values were increased with increasing composting period. High concentrations of NH₄-N were observed at the thermal phase and then decreased towards the end of composting, while the contents of NO₃-N showed an opposite trend. In this respect, a gradual increase in total nitrogen was observed, while organic matter, organic carbon and C/N ratio were significantly decreased as composting progressed. Decomposition rates of the organic matter increased and reached to its maximum values after the 4^th week. Meanwhile, application of natural amendments induced relatively high values of decomposition rates. Availability of both phosphorus and potassium were significantly increased throughout the decomposition period. Further improvements in the examined parameters were gained by application of the natural amendments and still more pronounced with EM addition. Salmonella and Shegilla counts dropped rapidly, being not detected at the end of composting. But a general increase in counts of phosphate dissolving bacteria throughout the composting process was observed especially in the amended treatments. Numbers of ammonifiers and nitrifying bacteria varied according to compost age, type of raw wastes as well as natural additives.