Microbial induced calcium carbonate precipitation (MICP) technology has been successfully used to enhance the properties of recycled concrete aggregates. However, the complex source and varied physical and chemical properties of recycled aggregates may have influence on the modification efficiency since microbes are often sensitive to the surroundings. In this study, two representative types of recycled aggregates, recycled concrete aggregates (RCA) and recycled brick aggregates (RBA), were subjected to two kinds of MICP treatments, basic MICP treatment and sodium alginate (SA) aided MICP treatment. The absorption and desorption of bacteria in/on aggregates during MICP treatments were quantified. The physical and chemical properties of aggregates after the bio-treatments were tested, and the influence of alkalinity and pore structure of aggregates under various MICP treatment methods on treatment efficiency were detailed investigated. Results indicated that, when the aggregates were subjected to the basic MICP treatment, the treatment efficiency was more remarkable in RBA, because of its high porosity and moderate pH (around 8–9), which facilitated the absorption of bacteria in/on aggregates and urease activity respectively. While under SA-aided MICP treatment, the influence of pore structure and alkalinity of aggregates on the treatment efficiency was not significant compared with that under the basic MICP treatment, especially the mass of CaCO₃ on the aggregates. The biogenic CaCO₃ generated by SA-aided MICP treatment not only plugged micropores, but also distributed all over the entire surface of the aggregates, resulting in a sufficient repair of microcracks. Meanwhile, the surface repair may reduce the influence of pore structure and pH of aggregates on the precipitation process, thereby reducing the impact of varied physical and chemical properties of aggregates on the treatment efficiency, which was conducive to the widely unified application of SA-aided MICP treatment in the modification of recycled aggregate based on construction solid waste.