This study aimed to evaluate the thermal stability of anthocyanins extracted from blackberry (Rubus spp.) and nanoencapsulated in a pectin-based structure associated with lysozyme by molecular self-assembly and observe the effects on cell viability, cytotoxicity, and in vitro absorption in fibroblasts. Anthocyanin bioaccessibility was evaluated using the INFOGEST static in vitro simulation of gastrointestinal digestion, and the colloidal stability, morphology, and protection of the nanoencapsulated anthocyanins were observed. The effects on fibroblast cells prepared in two and three-dimensional structures were observed. The major anthocyanin identified was cyanidin-3-O-glucoside. The nanoparticles showed homogeneity and spherical morphology with a particle mean diameter of 192.1 nm, PDI 0.10, Zeta Potential of −25.8 mV, and encapsulation efficiency of 79% with homogeneous and spherical morphology. The physical-chemical characteristics of the nanoparticles were maintained throughout different temperatures, and the anthocyanin degradation was statistically lower than that of isolated anthocyanin. In simulated gastrointestinal digestion, the size and stability of nanoparticles were maintained while protecting anthocyanins from digestion factors. No effects on fibroblast viability and cytotoxic effects were observed. It observed absorption of nanoparticles in the two cell models (2D and 3D). The nanoparticles were stable at different temperatures and in the simulated digestion. They were effectively absorbed in vitro, and there is no evidence of deleterious cell effects at a 5% concentration. The nanoencapsulated anthocyanin is indicated as a new potential technology for application in foods and supplements.