Urban-scale building energy modeling (UBEM)—using building modeling to understand how a group of buildings will perform together—is attracting increasing attention in the energy modeling field. Unlike modeling a single building, which will use detailed information, UBEM generally uses existing building stock data consisting of high-level building information. This study evaluated the impacts of three zoning methods and the use of floor multipliers on the simulated energy use of 940 office and retail buildings in three climate zones using City Building Energy Saver. The first zoning method, OneZone, creates one thermal zone per floor using the target building’s footprint. The second zoning method, AutoZone, splits the building’s footprint into perimeter and core zones. A novel, pixel-based automatic zoning algorithm is developed for the AutoZone method. The third zoning method, Prototype, uses the U.S. Department of Energy’s reference building prototype shapes. Results show that simulated source energy use of buildings with the floor multiplier are marginally higher by up to 2.6% than those modeling each floor explicitly, which take two to three times longer to run. Compared with the AutoZone method, the OneZone method results in decreased thermal loads and less equipment capacities: 15.2% smaller fan capacity, 11.1% smaller cooling capacity, 11.0% smaller heating capacity, 16.9% less heating loads, and 7.5% less cooling loads. Source energy use differences range from -7.6% to 5.1%. When comparing the Prototype method with the AutoZone method, source energy use differences range from -12.1% to 19.0%, and larger ranges of differences are found for the thermal loads and equipment capacities. This study demonstrated that zoning methods have a significant impact on the simulated energy use of UBEM. One recommendation resulting from this study is to use the AutoZone method with floor multiplier to obtain accurate results while balancing the simulation run time for UBEM.