Health systems of low-to-middle-income countries may have fewer buffering resources and capacity against shocks from a pandemic. This study assessed the effects of COVID-19 on essential health care services and its mitigation strategies employed in Benishangul Gumuz Region in the Assosa district of western Ethiopia. Institutional based cross-sectional study design with multilevel triangulated mixed approach was used. Purposively selected health facilities and key informant or in-depth interviewee from different facilities were involved. Document review from health facilities reports and case registration logs were used to access the service utilizations per-and -post the pandemic. The study showed that there was a significant decrement in antenatal care (ANC) visits, family planning new acceptors, family planning repeated acceptors, skilled delivery, and in postnatal care within 7 days of delivery during the COVID-19 pandemic. There was an increase in home delivery, teenage pregnancy and still births. There was also a significant reduction in the vaccination coverage for almost all vaccines. During the pandemic, children treated for diarrheal disease and the number of people screened for human immunodeficiency virus (HIV), new HIV-positive individuals, and new HIV-positive individuals receiving antiretroviral therapy have decreased significantly. There has been a statistically significant increase in the number of people with elevated blood sugar during the pandemic. The COVID-19 pandemic has had a significant negative impact on essential health services, most notably in Benishangul Gumuz Region. Groups of individuals considered to be at higher risks of morbidity and mortality are the most significantly affected. Mitigation strategies have been implemented to address the indirect effects of the COVID-19 pandemic and improve health care delivery in the region’s highly affected areas. Urgent and comprehensive action is needed to mitigate the future (long-term) impact of Covid-19 on the health of community in the region.