Microalgae production is expensive and demands high volumes of water and energy to meet all market demands and yet the production of secondary metabolites using alternative media needs deeper studies. Among alternative media, the use of sugar cane vinasse has gained attention for microalgae cultivation. In this work, we’ve compared the biomass yield and secondary metabolites of Chlorella sorokiniana grown in a commercial medium (Sueoka) and in alternative medium prepared with cane vinasse (0.1%) supplemented with N, P2O5 and K2O (commercial formula 20-5-20 g.L-1). The production of microalgae biomass grown in an alternative medium was 2.2% lower, but reached its maximum growth point 14 days faster than the commercial medium. The average level of Phenolic compounds on the commercial medium were 6.02 ± 0.13 mg GAE .g-1 and increased to 15.28 ± 0.32 mg GAE.g-1when C. sorokinianawere grown in the vinasse medium. Same how, Flavonoids contents varied from 13.12 ± 1.33 to 72.30 ± 5.28 mg QE. g-1 to commercial and vinasse medium, respectively. The maximum AOA of C. sorokiniana grown in vinasse medium was 88.05% at a concentration of 1500 µg.mL-1 of extract, with IC50 at 357.7 ± 27.35 µg.mL-1. Different factors seem to induce variances on secondary metabolites synthesis, mostly stress due to QOD and ions added to the medium by vinasse. The authors recognize there are more investigations to be done, but increasing a natural and low cost pathway for flavonoids yield open up an interesting field for the bioprospection of microalgae.