Magnesium ammonium phosphate cement (MAPC) prepared with ammonium dihydrogen phosphate (NH4H2PO4, ADP) and dead-burned Magnesium oxide (MgO) is a new type of rapid patch repair material for concrete structures. In order to reduce the material costs of MAPC mortar, manufactured limestone sands, being a more widely-available resource with lower cost, was investigated in this study as an alternative to quartz sands for the preparation of MAPC mortar. The limestone fines in manufactured sands were found to be the key factor that influences properties of MAPC mortar by causing bubbling and volume expansion before hardening. As a result, the mechanical strength of MAPC mortar decreased with the increasing content of limestone fines due to increased porosity. According to microstructure analysis, the mechanism of these negative effects can be inferred as the reaction between limestone fines and ADP with the gas generation of CO2 and NH3. This reaction mainly occurred during a short period before setting while most limestone fines remained unreactive in the hardened MAPC mortar. Based on the above detailed experimental findings on the effects of limestone fines in manufactured sand on the properties of MAPC mortar, this paper pointed out that effective defoaming methods for inhibiting bubbling was the key to the utilization of manufactured sands in preparation of high performance MAPC mortar.