In this work, the biomass productivity for biorefinery products and growth curves of three autochthonous microalgae collected in different reservoirs (“Scenedesmus sp.” (SSP), mixture of Scenedesmus sp., Chlorella minutissima, Chlorellas sp. and Nannochloropsis sp. named “La Orden” (LO) consortium and Chlorella minutissima named “Charca Brovales” (CB) consortium) were studied in a 5.5 L column laboratory photobioreactor. Two different culture media, Arnon culture (AM) and an agriculture fertilizer-based liquid medium (FM), have been used to evaluate the growth effect of the microalgae; it was found that the medium has a clear effect on the biomass productivity and growth rate, which ranged between 0.26−0.498 g L−1 d−1 and 0.288−0.864 d−1, respectively. In general, the elemental analysis and higher heating value of microalgae biomass for the three species were independent of the culture medium used for its growth, while their lipids and sugars content depended upon the species type and culture medium used in the cultivation. “La Orden” microalga was selected (given its best adaption to the climatic conditions) to study the biomass productivity and growth rate in two exterior photobioreactors (100 L column and 400 L flat panel), using FM as a medium, obtaining values of 0.116−0.266 g L−1 d−1 and 0.360−0.312 d−1, respectively. An automation and control system was designed to operate the exterior photobioreactors pilot plant. The lipid content of this microalga in these photobioreactors was lower than in the laboratory one, with a fatty acids profile with predominantly palmitic, oleic, linoleic and linolenic acids. Also, the fresh biomass collected from these photobioreactors was studied in a batch type digestion process for biogas production, obtaining a CH4 yield of 296 ± 23 L CH4 kgVSS−1 added with a reduction in percentage of COD and vs. of 50 ± 1% and 50 ± 1.7%, respectively.