In tissue engineering, stem cells have become an ideal cell source that can differentiate into most human cell types. Among the stem cells, bone marrow-derived stem cells (BMSCs) have been widely studied, and there is strong evidence that these cells can be differentiated into cells of the osteogenic lineage. Thus, BMSCs have become the gold standard for studies of tissue engineering in orthopedics. However, novel stem cell sources, such as amniotic fluid-derived stem cells (AFSCs) have been identified, and these have important and unique features that may lead to novel and successful applications toward the regeneration of bone tissue. This study was designed to originally compare the osteogenic potential of both BMSCs and AFSCs under distinct culture environments to determine whether the osteogenic differentiation process of both types of stem cells is related to the origin of the cells. Osteogenic differentiation was carried out in both two and three dimensions using a tissue culture plate and by means of seeding the cells onto microfibrous starch and poly(ɛ-caprolactone) scaffolds (a blend of starch and polycaprolactone), respectively. BMSCs and AFSCs were successfully differentiated into the osteogenic cell type, as cells derived from them produced a mineralized extracellular matrix. Nevertheless, the two types of cells presented different expression patterns of bone-related markers as well as different timing of differentiation, indicating that both cell origin and the culture environment have a significant impact on the differentiation into the osteogenic phenotype in AFSCs and BMSCs.