The physicochemical properties and structural characteristics of milk gels in deuterium oxide (D2O) induced by rennet and tamarillo enzyme (tamarillin) were investigated. SDS-PAGE showed that both proteinases hydrolysed κ-casein while tamarillin also exhibited a broader specificity on α- and β-casein. Small and large deformation rheological measurement showed that rennet-induced milk gels at low milk solid content (10% w/w) displayed higher elasticity than the gels induced by tamarillin. In high concentration milk gels (20% w/w), the aggregation time was sharply decreased and the elasticity was increased for both rennet and tamarillin induced gels. In addition, large deformation experiments indicated that rennet-induced gels are more brittle than those made with tamarillin for both 10 and 20% (w/w) milk gels. The microstructures of the milk gels displayed more porosity in the gels made with tamarillin, compared to those made with rennet, likely due to the broader caseinolytic activity of the tamarillin. Ultra-small angle neutron scattering (USANS) showed that there are no differences in the large-scale structure of tamarillin and rennet induced gels. However, small angle X-ray scattering (SAXS) revealed that the milk gel fine structures are different.