This paper outlines the experimental application of a continuous microwave-assisted (MW) industrial pilot plant for a post-harvest treatment on almond as disinfestation. The analysis of temperature uniformity and of the volatile profile on the unshelled almonds after the physical treatment were also investigated. The major problem during the production, storage and marketing of almonds is the contamination with insects or pests. Microwaves technologies is an alternative procedure to chemical one nowadays applied. The pilot plant has a treatment chamber with five generators of 1,5 kW/each installed along. A PLC operates on Electrical Power and flow rate to configure the operative parameter for the treatment condition. Samples of unshelled almonds from homogeneous batches have been treated with MW at different conditions. Insect mortality in three different life stages: 24-hours old eggs, 24-hours old larvae and mature larvae was evaluated after MW treatments. The uniformity of heating was studied as well as a volatile profile by SPME/GC/MS after the treatment. The results show that the optimal disinfestation effects on eggs and larvae are obtained by subjecting the almonds to a MW treatment at 25-rpm as spiral rotation speed equal to a 55.7 °C as temperature of the almond. The temperatures reached, during the treatment and the related time, were not sufficient for the development of oxidative aldehydes, secondary products of the lipid oxidation. An increase in volatile compounds, important for the characteristic almond flavour such as benzhaldeyde and 3-methylbutanol, has been observed.