Livestock wastewater represents both an environmental challenge and a potential nutrient source for microalgal bioprocesses. This study developed a sequential upstream–downstream strategy integrating wastewater-based cultivation of Chlorella vulgaris with ultrasound-assisted carotenoid recovery. A simplex-centroid mixture design was first used to evaluate slaughterhouse wastewater, swine wastewater, and Bold’s Basal Medium as cultivation components. Within the investigated mixture domain, 100% swine wastewater produced the highest cell concentration, with predicted and experimentally validated values of 5.08 × 10⁶ and 5.41 × 10⁶ cells mL⁻¹, respectively. Nutrient removal reached up to 97% for NH₄⁺–N, 40% for PO₄³⁻–P, and 92% for COD, depending on wastewater formulation. Subsequently, ultrasound-assisted carotenoid extraction was optimized using response surface methodology. The model-selected operating condition was 25% amplitude and 10 min; experimental testing yielded a spectrophotometric lutein-equivalent content of 116.80 mg kg⁻¹ and an extract purity index of 2.39, compared with model estimates of 118.47 mg kg⁻¹ and 2.42, respectively. The study demonstrates the laboratory-scale feasibility of experimentally linking wastewater formulation with subsequent pigment recovery while identifying analytical, energetic, and scale-up limitations requiring further investigation.