Microbial induced calcium carbonate precipitation (MICP) is a novel approach in the field of biocementation that is suitable for use in the construction industry. MICP has various applications which have already been well-researched, such as in soil improvement and self-healing concretes. This study shows an MICP surface treatment method to improve the properties of recycled aggregates. Due to the disadvantageous porosity properties of recycled aggregates, their use in recycled concrete is challenging. MICP treatment forms a calcium carbonate layer on the recycled aggregate’s surface to achieve a sealing effect. However, the MICP process also produces by-products such as ammonium salts which can affect the recycled aggregate concrete’s strength. The type of ammonium salt formed depends on the calcium source used during treatment. The calcium sources tested in the MICP process include: calcium chloride, calcium acetate, and calcium formate. Ammonium is known to decrease the compressive strength of concrete. To investigate this effect in recycled concrete in more detail, the ammonium content of the MICP-treated recycled aggregates was measured using eluate tests. Various rinsing strategies were carried out to examine the ammonium removed from the aggregates and the changes in the resulting compressive strength. The results show that both the ammonium concentration measured in the eluate and the calcium source used during treatment affect the mechanical properties of the concrete. Using an overhead shaker for rinsing was found to be highly effective in removing ammonium, resulting in an increase in the compressive strength of the recycled aggregate concrete.