Legume is a plant in the family of fabaceae (leguminoseae) which is present in diet of all people worldwide because they are good sources of starch, dietary fiber, protein, lipids and minerals. However, legumes contain large amounts of antinutritional factors (i.e. trypsin inhibitors, alpha-galactosidase, inositol phosphate) in the raw seeds that need to be reduced by processing before consumption. Germination has been suggested as a conventional and inexpenstive way to improve nutritional value of legumes. Nowadays, a great types of sprouts are offered in markets as healthy food and among them mung bean and clover sprouts are very popular products. Since sprouts are not often cooked before consumption, they are good vehicle for microbial contamination. Therefore, to minimize microbial contamination in the sprouts, initial microbial load should be controlled prior to consumption. Essential oils as natural santitizing agents could be used for this purpose. In this study, the change of chemical composition, antioxidant activity, total phenolic compounds, minerals, ascorbic acid and organic acids content were determined in raw, soaked and germinated mung bean and clover. Then clover and mungbean sprouts were treated with 0,0.5,1 and 2% concentration of thyme and 0, 1, 2 and 4% savory essential oils, respectively. Samples were stored at 4 during 10 days. The total microbial count, total coliforms and mold and yeast of samples were determined in 0, 1, 3, 5, 7 and 10 days. The results showed a significant increase in moisture, protein and ash and a significant reduction in fat and carbohydrate due to the energy consumption during 4-day germination. Total phenolic content and antioxidant activity indicated 2.5 and 1.5 fold increase in mung bean sprout and 2 and 1.5 fold increase in clover sprout compared to raw seed. Ascorbic acid content varied from 8.9 to 19.6% in mungbean and from 7.3 to 10.1% in clover sprouts. Analysis of fatty acids composition showed that mung bean sprout contained 17% and 36% linolenic and linoleic acids, respectively. The major component of clover oil is linoleic acid with 52%. The treated mung bean and clover sprouts were demonstrated significant reduction in total count, coliforms and mold and yeast followed by increasing essential oils concentration. In zero day, total count of mung bean and clover sprouts with 2% thyme and 4% savory essential oils showed 2.5 and 3.2 logarithmic cycle reduction against to controls, respectively. At the end of storage, this difference reached 1.7 in mung bean and 2 log cfu/g in clover sprouts. In general, results showed that mung bean and clover sprouts have more nutritional value than raw seeds and it is feasible to extend their shelf life with savory and thyme essential oils. Keywords : Clover, Mungbean, Sprout, Essential Oil, Microbial Load