Reclaimed water poses environmental and human health risks due to residual organic micropollutants and pathogens. Ozonation of reclaimed water to control pathogens and trace organics is an important step in advanced water treatment systems for potable reuse of reclaimed water. Ensuring efficient pathogen reduction while controlling disinfection byproducts remains a significant challenge to implementing ozonation in reclaimed water reuse applications. This study aimed to investigate ozonation conditions using a plug flow reactor (PFR) to achieve effective pathogen removal/inactivation while minimizing bromate and N-Nitrosodimethylamine (NDMA) formation. The pilot scale study was conducted using three doses of ozone (0.7, 1.0 and 1.4 ozone/total organic carbon (O3/TOC) ratio) to determine the disinfection performance using actual reclaimed water. The disinfection efficiency was assessed by measuring total coliforms, Escherichia coli (E. coli), Pepper Mild Mottle Virus (PMMoV), Tomato Brown Rugose Fruit Virus (ToBRFV) and Norovirus (HNoV). The ozone CT values ranged from 1.60 to 13.62 mg min L−1, resulting in significant reductions in pathogens and indicators. Specifically, ozone treatment led to concentration reductions of 2.46–2.89, 2.03–2.18, 0.46–1.63, 2.23–2.64 and > 4 log for total coliforms, E. coli, PMMoV, ToBRFV, and HNoV, respectively. After ozonation, concentrations of bromate and NDMA increased, reaching levels between 2.8 and 12.0 μg L−1, and 28–40.0 ng L−1, respectively, for average feed water bromide levels of 86.7 ± 1.8 μg L−1 and TOC levels of 7.2 ± 0.1 mg L−1. The increases in DBP formation were pronounced with higher ozone dosages, possibly requiring removal/control in subsequent treatment steps in some potable reuse applications.