Storage of food stuff and cereals has been a global issue from years due to fungal infection and development of mycotoxins; the most dangerous are aflatoxins, which not only deteriorate the food quality but have carcinogenic potential for mammals. In view of nutritive value and potential of plants as safer and viable source of antifungal agents, the present research work has been designed to evaluate the antifungal activities of various agricultural wastes and some medicinal plants against the aflatoxigenic strains of Aspergilus flavus and Aspergillus parasiticus, so as to reduce the aflatoxin production in cereal grains durin storage. The antifungal components of plants were extracted using solvents like methanol, ethanol, chloroform and acetone. Antifungal activity determined by Disc Diffusion method and Minimum Inhibitory Concentration (MIC) showed that ethanolic extract of pomegranate peels exhibited highest antifungal effect against both tested fungi with maximum zone of inhibition 38 mm for A. paracitus and 37 mm for A. flavus, however, the least effect was observed by ethanolic extract of sugarcane baggasse with minimum DIZ value of 10 mm against both fungi. Crude extracts having good antifungal activity were analyzed for antifungal constituents (phenolic acids) by GC-MS. Total of 8 phenolic acids like gallic acid, cinamic acid, benzoic acid, vanillic acid, protocacheuic acid, ferulic acid, caffeic acid, and para-coumaric acid were identified on the basis of availability of standard chemicals and spectral data. Significant variation (P<0.05) was found among concentration of phenolic acids detected in different tested plant extracts. The cereal grains (wheat, maize and rice) inoculated with A. flavus and A. parasiticus were stabilized with 5 plant materials at three different concentrations (5, 10, and 20%) and stored at two different conditions of temperature and moisture (25 o C temperature and 18% moisture and 30 o C temperature and 21% moisture) for a period up to 9 months. After regular interval of time, qualitative analysis by TLC and quantitative estimation by HPLC was performed. Among the investigated plants pomegranate peels and neem leaves (20 %) were found to be most effective and they fully inhibit aflatoxin B 1 synthesis (100%) by both tested fungi at all cereals (maize and rice and wheat) and B 2, G 1 and G 2 synthesis at 25 o C temperature and 18% moisture level. Whereas, at high temperature and moisture level (30 o C and 21%) neem leaves and pomegranate peels fully inhibited aflatoxin B 1 synthesis by both tested fungi in wheat and maize but did not show complete inhibition of aflatoxin B 1 synthesis in rice. Generally the order of inhibitory potential of investigated plants at 20 %concentration against aflatoxins synthesis by both tested fungi was as neem leaves > pomegranate peels > citrus leaves > citrus peels > kikar leaves. Finally statistical analysis was applied on triplicate optimized samples using mean, standard error, and analysis of variance ANOVA. Significant differences of mean were calculated using Least Square Difference (LSD) test. Overall results of the current study showed that neem leaves and pomegranate peels can be used directly or to develop agents to control the production of aflatoxin in cereals effectively in controlled moisture and temperature conditions.