Biofuel production from microalgae non-food feedstock is a challenge for strengthening Green energy nowadays. Reviewing the current technology, there is still reluctance in investing towards the production of new algal strains that yield more oil and maximize capital gains. In the current work, the microalgal feedstock selection problem is investigated for increased lipid production and nano-catalytic conversion into clean biofuel. For that purpose, a variety of Fuzzy Multi-Criteria Decision Making processes and a multitude of Optimization criteria spanning to technological, environmental, economic, and social aspects are used. The strains selected for the analysis are Chlorella sp., Schizochytrium sp., Spirulina sp., and Nannochloropsis sp. The methods applied are fuzzy analytic hierarchy process, FTOPSIS (fuzzy technique for the order of preference to the ideal solution), and FCM (fuzzy cognitive mapping). Pairwise comparison matrices were calculated using data from extensive literature review. All aforementioned fuzzy logic methodologies are proven superior to their numeric equivalent under uncertain factors that affect the decision making, such as cost, policy implications, and also geographical and seasonal variation. A major finding is that the most dominant factor in the strain selection is the high lipid content. Moreover, the results indicate that the Chlorella Vulgaris microalgae is ranked as the best choice by the FTOPSIS method followed by the Nannochloropsis strain, and Spirulina Platensis was found to be the last in performance. The best and worst case scenario run with FCM experimentally verify this choice indicating that Chlorella Vulgaris follows this trend of selection mostly with the technological and the economic criteria for both the sigmoid and the hyperbolic tangent deep-learning functions used.