The winery industry generates a large volume of wastewater characterized by high concentration of phenolic compounds, ethanol concentration of around 14 g/L, acidic pH (close to 4), and intense coloration. These characteristics pose environmental challenges, require requiring treatment before wastewater discharge and may inhibit biological remediation processes. This study proposes an integrated pre-treatment strategy for winery wastewater, aiming to mitigate its toxicity and enable its reuse as a culture medium for microalgae. The approach focuses on reducing the use of chemical agents and minimizing the need for wastewater dilution by employing sustainable techniques, such as air bubbling and pH neutralization using alkaline residues from biomass thermoelectric plants and from meat and bone meal incineration. The pre-treatment was conducted in two main stages. First, ethanol removal was achieved through air bubbling for five days. Second, pH neutralization and organic load reduction were performed using alkaline residues. The effectiveness of biomass ash and bone and meal ash was compared regarding their capacity to neutralize the wastewater, precipitate organic compounds, and retain essential nutrients. The results obtained indicate that biomass ash was more effective in neutralizing the wastewater, requiring 10 g/L to reach pH 7, while bone meal ash demanded approximately four times this amount. Biomass ash also achieved a significant reduction in chemical oxygen demand (COD) and phenolic compounds (around 90%). However, it caused a considerable depletion of key nutrients, particularly nitrates and phosphates, which are essential for microalgae growth. In contrast, bone meal ash preserved these nutrients more effectively due to its high phosphorus content, which not only prevented phosphate depletion but also enriched the medium. Additionally, bone ash resulted in a less colored wastewater (52.3–67.7% color reduction), which is critical for light penetration and microalgae photosynthesis. This study demonstrates that the use of alkaline residues for winery wastewater pre-treatment can effectively mitigate the toxic effects while promoting resource valorization. Bone meal ash emerged as a promising agent due to its ability to maintain nutrient availability and reduce turbidity, enhancing the wastewater’s suitability as a microalgae culture medium. This approach aligns with circular economy principles by repurposing industrial residues that are still being deposited in landfills and providing a sustainable solution for managing winery waste streams while facilitating microalgae-based biotechnological applications.