Background and objectives: Wheat grain has an important value in the world nutrition. Evaluating the physical and microbial properties of agricultural products plays an important role during harvesting with machines, cleaning process and waste reduction. In this study, for the first time in Iran, the optimized effects of cleaning and moisture content at 40oC on the physical (useful besatz, unuseful besatz, hectoliter, thousand seed weight) and microbial (total count of bacteria and molds) properties of wheat grain (n-80 variety) in Golestan province, were modeled.Materials and methods: After determining the basic moisture content, samples with three levels of cleaning (0-100%), and different moisture contents (10-14% w.b) at 40oC were studied and modeled by response surface methodology using central composite design (face center) including 21 tests with five repeats at the central point.Results: The results showed that by reducing moisture content and increasing cleaning levels, useful and unuseful besatz decreased and hectoliter increased. Also increasing the cleaning percentage was more effective than moisture content reduction in reducing useful besatz and unuseful besatz. The lowest value of hectoliter was 72.58 (0.01kg. lit-1) at 40oC. The highest thousand seed weight at moisture content 14% (w.b) and cleaning level 100%, was 36.80 gr. Higher rate in increase in thousand seed weight was found in the higher moisture content than that in the higher level of cleaning. With increasing moisture content and reduction in cleaning level, total microbial count increased. Linear parameters of cleaning and moisture had a significant effect (p < 0.01) at 40oC on the total count of microorganisms in the linear model. Total microbial count increased by 52.7 and 90%, at moisture content 14% (w.b) and cleaning level of 10%, respectively in comparison to that in moisture content 10% (w.b). R2 for useful besatz, unuseful besatz, hectoliter, thousand seed weight, total counts of microorganisms and molds (colony/g) were 0.9463, 0.9818, 0.9677, 0.8255, 0.8547 and 0.9674, respectively. The results of optimization at 40oC showed that cleaning level of 100% and moisture content of 10% (w.b) resulted in storage of grain wheat with desirability of 94.1%.Conclusion: Regard to non-significant lack of fit and high values of R2 and adjusted R2, our selected models could accurately predict the experimental values for all studied properties.