In the present work, microalgae strains, such as Scenedesmus obliquus and Phaeodactylum tricornutum grown in indoor/outdoor photobioreactors (PBRs) and in open ponds (this is the first study on such strains cultivated in the local Southern Italy climatic conditions), were fully analyzed for their protein content, carbohydrates, lipids, and fatty acid profile in order to assess their potential use for the production of biofuels, chemicals, and omega-3, and as animal feed and human food. They are compared with Nannochloropsis sp. (commercial sample) which was fully analyzed in our laboratory and Chlorella (literature data). An economic evaluation was carried out, demonstrating that the cultivation of microalgae for the production of only biofuels will not match the economic standards. Conversely, if chemicals are also produced applying the biorefinery concept and using wastewater as a source of nutrients, it will be possible to have a good positive return from microalgae.