Seismic activity in the eastern region of Indonesia, particularly in Ambon, has been a matter of great concern because of its high tectonic activity. The devastating magnitude 6.5 earthquake in September 2019, which resulted in fatalities and significant damage, highlighted the region’s vulnerability and emphasized the importance of understanding the area’s seismic hazards. Although previous studies have been conducted, this study aims to fill critical gaps in the literature by using the latest seismic data until 2022 and updated attenuation equations. Disaggregation analysis is employed to identify ground motion characteristics, that are crucial for calculating synthetic ground motion acceleration. Under risk-targeted maximum considered earthquake (MCER) conditions, the study results show a peak ground acceleration of 0.444 g, with spectral acceleration at 0.2 s reaching 1.093 g, which decreases to 0.350 g at 1.0 s. Notably, background earthquake sources play a dominant role in contributing to the region’s high seismic hazard potential. The results of this study highlight the urgency of updating Indonesia’s national seismic hazard map. The study also recommends future studies to explore additional parameters of newly discovered faults to enhance understanding of fault movements and their impacts in the study area.