A growing number of cities and regions are promoting or mandating on-site treatment and reuse of wastewater, which has resulted in the implementation of several thousand on-site water reuse systems on a global scale. However, there is only limited information on the (microbial) water quality from implemented systems. The focus of this study was on two best-in-class on-site water reuse systems in Bengaluru, India, which typically met the local water quality requirements during monthly compliance testing. This study aimed to (i) assess the microbial quality of the reclaimed water at a high temporal resolution (daily or every 15 min), and (ii) explore whether measurements from commercially available sensors can be used to improve the operation of such systems. The monitoring campaign revealed high variations in microbial water quality, even in these best-in-class systems, rendering the water inadequate for the intended reuse applications (toilet flushing and landscape irrigation). These variations were attributed to two key factors: (1) the low frequency of chlorination, and (2) fluctuations of the chlorine demand of the water, in particular of ammonium concentrations. Such fluctuations are likely inherent to on-site systems, which rely on a low level of process control. The monitoring campaign showed that the microbial water quality was most closely related to oxidation–reduction potential (ORP) and free chlorine sensors. Due to its relatively low cost and low need for maintenance, the ORP emerges as a compelling candidate for automating the chlorination to effectively manage variations in chlorine demand and ensure safe water reuse. Overall, this study underscores the necessity of integrating treatment trains, operation, and monitoring for safe on-site water reuse.