Yogurt-based snacks originally with a calcium content between 0.10 and 0.17 mmol/g dry matter were enriched with a whey mineral concentrate and whey protein isolate or hydrolysate. Whey mineral concentrate was added to increase the total amount of calcium by 0.030 mmol/g dry matter. Calcium bioaccessibility was determined following an in vitro protocol including oral, gastric, and intestinal digestion, with special focus on the effect of lime juice quantifying calcium concentration and activity. Calcium bioaccessibility, defined as soluble calcium divided by total calcium after intestinal digestion amounted to between 17 and 25% for snacks without lime juice. For snacks with lime juice, the bioaccessibility increased to between 24 and 40%, an effect attributed to the presence of citric acid. Citric acid increased the calcium solubility both from whey mineral concentrate and yogurt, and the citrate anion kept supersaturated calcium soluble in the chyme. The binding of calcium in the chyme from snacks with or without lime juice was compared electrochemically, showing that citrate increased the amount of bound calcium but with lower affinity. The results indicated that whey minerals, a waste from cheese production, may be utilized in snacks enhancing calcium bioaccessibility when combined with lime juice.