Changes in the fatty acid profile and the microstructure of avocado puree after microwave treatment were evaluated. The main components of the fatty acid profile were oleic, palmitic, linoleic and palmitoleic acids. Fatty acids profile of microwaved avocado puree did not show significant changes (p < 0.05). Trans fatty acids were not detected. Microwaved avocado puree showed significant changes in its microstructure. Samples treated with microwaves for less than 40 s preserved the cells shape, causing only a minimal modification. On the other hand, microwave treated avocado puree using more than 40 s, showed a disruption of idioblast oil cells, releasing the oil contained on them. The results might be explained based on the sensory evaluation that was performed on the microwaved avocado puree, where samples at 60 s showed oily texture and grassy flavor.