The utilization of superabsorbent polymers (SAPs) in cement-based materials has been found to be a promising means of mitigating the autogenous propagation of shrinkage and cracks. On the other hand, the undesired effects of SAPs’ application on functional properties, including mechanical strength, microstructure formation, and the evolution of hydration heat are not properly understood, given the variety in SAPs’ characteristics. To contribute to the present state-of-the-art, cement mortars, modified with two grades of SAPs by dosages of 0.3%, 0.6%, and 0.9%, were designed and studied with emphasis on the relationship between the materials’ porosities and mechanical strengths. The obtained results are interpreted by scanning electron microscopy analysis and hydration heat evolution to elucidate the major changes and their driving factors. Besides the benefits associated with the mitigation of autogenous shrinkage, the achieved results point to an adverse effect of supplementation with SAP on mechanical strength at an early age, and an even more pronounced increase at a later age. The employed scanning electron microscopy images, together with mercury-intrusion porosimetry data, depict distortion in the material porosity as a result of the filling of formed voids and the closing of open ends by swelled hydrogels. Only the minor benefit of a greater cross-linking density was obtained by the formation of dense structures and the gains in mechanical strength therefrom.