The encapsulation of genetically modified cells represents a promising approach for the delivery of therapeutic proteins. The functionality of the device is dependent on the characteristics of the biomaterials, the procedures used in its confection and the adaptability of the encapsulated cells in the host. We report conditions leading to the development of calcifications on the polyvinyl alcohol (PVA) matrix introduced in hollow fiber devices for the encapsulation of primary human fibroblasts implanted in mice. The manufacturing procedures, batches of PVA matrix and cell lineages were assessed for their respective role in the development of the phenomenon. The results showed that the calcification is totally prevented by substituting phosphate-buffer saline with ultra-pure sterile water in the rinsing procedure of the matrix. Moreover, a positive correlation was found, when comparing two fibroblast cell lineages, between the level of lactate dehydrogenase (LDH) activity measured in the cells and the degree of calcium deposition. Higher LDH activity may decrease calcium depositions because it generates in the device a more acidic microenvironment inhibiting calcium precipitation. The present study defines optimized conditions for the encapsulation of primary human fibroblasts in order to avoid potentially detrimental calcifications and to allow long-term survival of encapsulated cells.