Pectin is used in dairy products to improve texture, but it may also affect calcium absorption. The influence of pectins with different degrees of esterification on calcium bioaccessibility in yogurt snacks enriched with or without whey mineral concentrates and lime juice was quantified using a three-step in vitro digestion including electrochemical determination of free and complex bound calcium. Calcium from whey minerals became bioaccessible under intestinal conditions when combined with lime juice, as a consequence of a large fraction of complex bound calcium by citrate. Pectin improved the texture of the snacks but lowered the calcium bioaccessibility by 6%–16% depending on the degree of esterification through endothermic binding of calcium to carboxylate groups of pectins as evidenced by higher yield stress of the snack bases. Decreasing degree of esterification and increasing blockiness promoted calcium binding, as indicated by the estimated binding sites and association constants. Increasing temperature from 25 °C to 37 °C and pH from 4 to 7 (intestinal conditions) also increased the interactions between calcium and pectins. For low methoxyl pectin, the complex binding of calcium to pectin carboxylates was found more evident than binding to citrate from the lime juice reducing calcium bioaccessibility. For high methoxyl pectin with fewer binding sites, citrate binding kept calcium available for uptake through intestinal digestion. A balanced formulation with whey minerals, lime juice and calcium-insensitive high methoxyl pectin yielded crispy yogurt snacks with high calcium bioaccessibility, which provides a new perspective to design dairy products with high nutritional value.