Microalgae when subjected to nutrient restriction conditions, inducing environmental stress, are prone to total lipid accumulation and changes in the fatty profile. In this context, the green microalgae Chlamydomonas sp. was submitted for 3 days to the absence of nutrients. Thus, the efficacy of the extraction of the crude hexane lipid fraction (CHF), using mechanical stirred associated with ultrasound technique, was evaluated in two different times (2 and 4 h), using scanning electron microscopy and thermogravimetric analysis (TG). Saponifiable fractions, CHF extracts and crude chloroform fraction (CCF) were esterified and characterized by TG, FTIR and GC/MS to identify their fatty profile. Residual biomass (RB) was analyzed by elemental analysis, and the resulting data were employed to estimate the higher heating value (HHV) and crude protein percentage. The micrographs of the biomass surfaces before and after the extraction process showed significant fragmentation only for the time of 4 h. A pronounced mass loss in the typical lipid range was evidenced by TG being consistent with the significant difference of material extracted in the time of 2 h (2.95 ± 0.28)% and 4 h (10.54 ± 0.46)%. The total lipid fraction (CHF and CCF) was approximately 29%. The RB revealed values of HHV and crude protein of 18 MJ kg−1 and 56%, respectively. The TG data for the CCF extract revealed a material consisting mainly of saponifiable fractions, unlike CHF which is composed predominantly of unsaponifiables. Therefore, the TG curve ratified a better conversion rate to CCF (approximately 89%), consistent with the value obtained by GC/MS (about 86%). The fatty profile for the saponifiable fractions of both extracts showed that the major fatty acids are C16:0 and C18:3 (ω-3 and ω-6). The ester profile with elevated concentration of polyunsaturated fatty acids (C18:3) is unfeasible in their application for biodiesel production; nevertheless, the fatty profile of microalgae suggests pharmacological potential for diet or therapy, since some of the main components are reported as bioactive metabolites.