Humanity is facing some major global threats, namely lack of environmental sustainability, the energy crisis associated with the unsustainable reliance on fossil fuels, and water scarcity, which will be exacerbated with the rapid growth of urban areas. Researchers have drawn their attention to microalgae, photosynthetic microorganisms known for their environmental applications, such as wastewater remediation and lipids accumulation, to produce third-generation biofuels to solve some of these major issues. Considering this dual role, this study evaluated the potential of the microalga Chlorella vulgaris on nutrient removal from a paper industry effluent and bioenergy production. Firstly, experiments were performed to assess the potential of this microalga to: (i) successfully grow in different concentrations of a paper industry effluent (20% to 100%); and (ii) treat the industrial effluent, reducing phosphorus concentrations to values below the accepted legal limits. Then, a techno-economic assessment was performed to study the viability of a C. vulgaris biorefinery targeting the remediation of a paper industry effluent and bioenergy production. The results have shown that C. vulgaris was able to successfully grow and treat the paper industry effluent. Under these conditions, average biomass productivities determined for this microalga ranged between 15.5 ± 0.5 and 26 ± 1 mg dry weight (DW) L−1 d−1, with maximum biomass concentrations reaching values between 337 ± 9 and 495 ± 25 mg DW L−1 d−1. Moreover, final phosphorus concentrations ranged between 0.12 ± 0.01 and 0.5 ± 0.3 mg P L−1, values below the legal limits imposed by the Portuguese Environment Agency on the paper industry. Regarding the proposal of a microalgal biorefinery for the bioremediation of paper industry effluents with bioenergy production, the techno-economic study demonstrated that six of the seven studied scenarios resulted in an economically-viable infrastructure. The highest net present value (15.4 million euros) and lowest discounted payback period (13 years) were determined for Scenario 3, which assumed a photosynthetic efficiency of 3%, a lipids extraction efficiency of 75%, and an anaerobic digestion efficiency of 45%. Therefore, it was possible to conclude that besides being economically viable, the proposed biorefinery presents several environmental benefits: (i) the remediation of an industrial effluent; (ii) CO2 uptake for microalgal growth, which contributes to a reduction in greenhouse gases emissions; (iii) production of clean and renewable energy; (iv) soil regeneration; and (v) promotion of a circular economy.