The current study investigated the effects of thermal processing of the microwave technology on nutritive value, crude protein solubility, urease activity and amino acid profile on linseed grains. Samples were treated in a SAMSUNG GE82N-B microwave oven at 450W for 0 (L1), 60 (L2), 180 (L3), 300 (L4), and 420 (L5) seconds, respectively. Microwave treatment for 300 seconds showed a significant (p ≤ 0.05) decrease in activity urease comparing to raw linseed. The raw and treated linseed protein solubility index (PDI) show statistical differences (p ≤ 0.05) between all the treatments compared. High performance liquid chromatography (HPLC) analyses of samples differences in the amino acid composition between controls and experimental treatments showed that amino acids were not significantly affected (p ≥ 0.05), except isoleucine and leucine amino acid (p ≤ 0.05). From the results of the present study, it is possible to identify that the best method for improving linseed quality for animal feed is the application of microwave for 60 second (treatment L2). Our results indicate that microwave thermal processing or micronizing dry thermal processing of grains could be successfully used in large industrial feed production with a short period of time and the improved nutritional parameters of grains, increased shelf-life and the unchanged amino acid profile of treated grains.