This study explored the cultivation of Porphyridium cruentum using beet molasses and corn steep liquor (CSL) as alternative agri-waste substrates. The objective was to enhance the biomass and lipid production of P. cruentum, known for its potential as an industrial EPA producer. Using a Box-Behnken Design (BBD) as part of the response surface methodology (RSM), we investigated the effects of beet molasses, CSL, and F/2 nutrients on the microalga's cultivation. The results demonstrated a significant influence of these factors on the final cell count and lipid content over an 8-day cultivation period. Specifically, optimal growth conditions were identified at approximately 1.78 g/L of molasses and 1.89 g/L of CSL, yielding a cell count of 12.1 × 106 cells/mL and a lipid content of 24.48%. Validation experiments reaffirmed these findings, with observed results closely aligning with predicted values. Optimized media achieved also a significant higher content of carotenoids and phycobiliproteins compared to the standard media. This research highlights the potential of using agro-industrial by-products for large-scale cultivation of P. cruentum, offering a sustainable approach for enhancing lipid and pigment production.