The amount of solid and liquid organic waste and wastewater is continuously increasing all over the world. The necessity of their reuse and recycling is, therefore, becoming more and more pressing. Furthermore, the limited fossil fuel resources, in conjunction with the need to reduce greenhouse gas emissions, advocate the production of renewable fuels. In this work, we analyze a sustainable second-generation process to produce biodiesel by transesterification of waste cooking oil, coupled with a third-generation process in cascade for recycling the incoming wastewater. Since this latter is rich in glycerol, it is used as a feed for microalgae, from which oil can be extracted and added to the waste cooking oil to further produce biodiesel and close the cycle. We studied the influence of different factors like temperature, catalyst load, and reactants ratio on the kinetics of transesterification of the waste oil and estimated the kinetic parameters by different kinetic schemes. The obtained values of activation energies and pre-exponential factors at chosen conditions of T = 60 °C and catalyst load of 0.6% w/w in methanol are: Ea,direct = 35,661 J mol−1, Ea,reverse = 72,989 J mol−1, k0,direct = 9.7708 [dm3 mol−1]3 min−1, and k0,reverse = 24,810 [dm3 mol−1]3 min−1 for the global fourth-order reversible reaction scheme and Ea = 67,348 J mol−1 and k0 = 2.157 × 109 min−1 for the simplified pseudo-first-order irreversible reaction scheme; both in strong agreement with literature data. Furthermore, we designed very efficient conditions for discontinuous and continuous operating mode, both at lab-scale and pilot-scale. The quality of the biodiesel produced from waste cooking sunflower oil is compared with that of biodiesel produced by different kinds of virgin vegetable oils, showing that the former possesses acceptable quality standards (Cetane number = 48 and LHV = 36,600 kJ kg−1). Finally, the recycling of wastewater rich in glycerol as a nutrient for mixotrophic microalgae nurturing is discussed, and microalgae growing kinetics are evaluated (k1 about 0.5 day−1), endorsing the possibility of algae extraction each 4–5 days in a semi-continuous operating mode. The experimental results at the pilot scale finally confirm the quality of biodiesel, and the obtained yields for a two-stage process prove the competitiveness of this sustainable process on the global market.