Microalgae, like plants, contribute significantly to the development of the oxygen biogeochemical cycle due to their high photosynthetic efficiency. In addition, they provide high yields of polyunsaturated fatty acids, sterols, proteins, terpenoids, and pigments, among others. Therefore, different species of microalgae have been studied and used on a laboratory scale to carry out processes such as wastewater treatment or aerobic bioconversion, which are presented as sustainable and viable alternatives for the treatment and recovery of organic waste (OW), usually rich in carbohydrates, lipids and proteins. In the present investigation, the removal of organic matter was evaluated during the adaptation of Nannochloropsis oculata in residues of poultry wastewater and swine origin, obtained from technical and semi-technical plants, respectively, located in the high mountain zone of the state of Veracruz, Mexico. The experiment was carried out in 250 mL discontinuous photobioreactors with a working volume of 200 mL, where 3 inoculum-substrate ratios were studied for each organic residue: 10, 15 and 20% inoculum in poultry wastewater (PWW) and 30, 50 and 70% inoculum in pig manure (PM). In addition, the conditions of temperature (20 ± 2 °C), illumination (2000 lx), photoperiod of 12/12 (light/dark) and continuous aeration were controlled. It was shown that N. oculata can tolerate alkaline conditions of pH ≥ 10 and contributes to the reduction of soluble organic matter in OW. PWW and PM were found to be viable media for the survival of N. oculata. Finally, regarding the inoculum concentrations studied, the most appropriate were 10% for PWW and 70% for PM.