The effects of an enzymatic treatment with cellulase and mannanase on the properties of marine microalgae Nannochloropsis sp. were investigated. The combined use of these enzymes synergistically promoted the recovery of lipids from the microalgae, increasing the extraction yield from 40.8 to over 73%. Untreated and enzymatically treated microalgae were characterized by chemical analysis and by TGA/DTG, FTIR, XRD and SEM. Significant changes were observed in the chemical composition and thermal behavior of the microalgae. The enzymatic treatment also resulted in an increase of the crystalline-to-amorphous cellulose ratio. SEM images revealed dramatic changes in cell morphology, extensive cell damage and release of intracellular material. Overall, the results obtained indicate that the enzymes used are capable of disrupting the microalgal cell wall and that a combination of common analytical techniques can be used to assess the enzyme-induced damage.