Moringa seeds have high medicinal and value nutritional. This is mainly to the large stock of biologically active ingredients in seeds. With the global shortage of food grains, the incidence of nutritional deficiency diseases and the ever-increasing population, Moringa in particular will certainly provide a good alternative to make up for the food shortage. This research aimed to study the effect of soaking process in water and in NaOH 0.5% solution on the Moringa seeds. Gross chemical composition, minerals, anti nutritional and fatty acid of M. oleifera and peregrina seeds were investigated. In general, Soaking has a significant (p <0.05) effect on the gross chemical of M. oleifera M. peregrina seeds. There is a large variation in minerals value both of raw and soaked Moringa oleifera and Moringa peregrina kernels. Results revealed that crude extract obtained from both of raw Moringa (oleifera and peregrina) seeds showed that there was a significant difference in anti-nutritional content before and after soaking. The aqueous soaking treatment was more effective than soaking with alkali solution NaOH 0.5% to remove anti nutritional factors. Furthermore, fatty acid oleic (C18:1) represented the highest proportion of fatty acids. Results indicated that soaking processes caused a significant decrease in total unsaturated fatty acids content, accompanied by an apparent increase in the total saturated fatty acids of M. oleifera and Peregrina seeds.