Calcium and phosphorus bioavailability from different milk-based (whole milk, skimmed milk and soya milk) fruit beverages as affected by thermal treatment (TT) and high-pressure processing (HPP) was determined by means of the paired in vitro gastrointestinal digestion (solubility method)/Caco-2 cell model. Ca bioaccessibility was significantly higher in HPP (98.4%±1.6%) versus TT (91.3%±1.9%), but Ca bioavailability was equal in all different matrixes independently of the processing treatment used. HPP samples improved P bioaccessibility (98.7%±2.5% versus 87.3%±2.2%) and P bioavailability by Caco-2 cells versus TT samples— soya milk- andwholemilk-based beverages being the sampleswiththe highest bioavailability values (56.8%±1.3% and 40.1%±9.9% versus 15.0%±2.1% and 16.8%±2.8%, respectively). Therefore, HPP improves Ca and P bioaccessibility, and P bioavailability versus TT samples, and can be used as an alternative to TT in themanufacture of functional foods with improved nutritional value and health benefits.