This work evidenced the insecticidal activity of encapsulated Mentha spicata essential oil (EO) against Rhyzopertha dominica in presence of stored wheat grain and evaluated the residual EO amount in wheat grains after treatment. EO distribution in the different fractions recovered after grain milling was also determined. The mortality rate against R. dominica reached more than 90% and was dependent on the amount of EO released from the encapsulation matrix. The quantification of the two major compounds of EO, (R)-limonene and (R)-carvone, showed that wheat grains contained different amount depending on the storage conditions. When wheat grains were stored in open jars, the EO residual amount in grains was especially low (1.98 mg/kg) compared to amount in closed jar (51.6 mg/kg). The flour resulting from milling contained lower amount of EO compounds in comparison with the bran fractions. The contact of wheat grains with EO clearly modified the native aromatic profile of the wheat flour as the most represented compounds were those belonging to the EO. In the native flour, ten volatile compounds, mainly alcohols and aldehydes due to oxidation of lipids were identified, which represented only 14% of the aromatic profile when the wheat grains were treated by EO. However, when the storage condition of grains mimics the silos conditions, the level of (R)-carvone, the major component of spearmint EO is found around 3 mg/kg of flour which was far below its currently use in bakery products.