The study of the properties of engineered rocks is of great importance to researchers in engineering sciences such as petroleum, mining, and civil engineering owing to their wide application in these fields. In the present study, a physico-chemical and geomechanical investigation was carried out on the effects of different clay minerals on porous rocks. Various chemical products formed during chemical interactions between cement, clay minerals, and water can change the pore structure and thus the rock characteristics. The results of the current study showed that increasing the clay content could remarkably reduce the porosity and permeability of the rock by an average of 86% and 6.76%, respectively. In this regard, samples containing kaolinite were further influenced due to their new pore structure. Moreover, a power relationship was found between sonic velocity and porosity, which can be used to predict rock properties. Chemical analysis indicated an amplification in quantities of chemical products, particularly calcium silicate hydrate and portlandite, due to an increase in clay content. The impacts of porosity and cementation quality as two main factors on rock strength have also been studied. The outcomes revealed that a reduction in porosity could compensate for detrimental effects of poor bond quality and consequently improved UCS by up to 30% in samples containing kaolinite, while decreasing the degree of cementation prevailed over the porosity reduction in specimens including illite and resulted in a 14% decrease in UCS. The effects of porosity and bond quality on UCS would cancel each other out in samples containing bentonite. It is worth noting that when it comes to changes in geomechanical characteristics, the dominant factor (i.e., porosity reduction or cementation quality) determines the ultimate effect of clay minerals on the properties of engineered porous rocks.