Abstract Background The overuse of antibiotics in primary healthcare settings (PHSs) has caused a serious public health problem in China. The outbreak of the Coronavirus Disease-19 (COVID-19) pandemic brought about dramatic changes in the supply of and demand for medical services in PHSs, possibly resulting in unprecedented changes in antibiotic use. Objective This study aims to assess the immediate and long-term impacts of the COVID-19 pandemic on the changes in antibiotic consumption in PHSs. Method The data on antibiotic consumption were collected from selected township hospitals in Shandong, China from January 2019 to December 2021. Antibiotic consumption was quantified by using the defined daily doses (DDDs) and the WHO Access, Watch, Reserve category. A segmented regression model was established to analyze the immediate and long-term impacts of the COVID-19 pandemic on antibiotic use by using the interrupted time series analysis. Results The overall antibiotic consumption in all PHSs decreased by 32.04% and 16.69% in 2020 and 2021 respectively compared to the corresponding period in 2019. Over the entire study period, the use of penicillins (J01C) and cephalosporins (J01D) accounted for more than 50% of the total antibiotic consumption. The average annual consumption of Watch category antibiotics decreased by 42.02% and 33.47% in 2020 and 2021 respectively compared to that in 2019. According to the interrupted time series analysis, the total antibiotic consumption decreased significantly immediately after the COVID-19 pandemic outbreak (coef. = − 2.712, p = 0.045), but it then increased significantly over a long-term (coef. = 0.205, p = 0.005). Additionally, the consumption of Access category antibiotics increased significantly in PHSs in the long-term (coef. = 0.136, p = 0.018). However, the consumption of Watch category antibiotics declined sharply immediately after the pandemic (coef. = − 1.222, p < 0.001), but then it increased slightly over a long-term (coef. = 0.073, p < 0.001). Conclusion The extensive use of penicillin and cephalosporins should be of great concern. After the outbreak of COVID-19 pandemic, the total antibiotic consumption decreased generally and the use pattern was improved to some extent in the PHSs in Shandong, China. This provides an opportunity for improving the misuse of antibiotics in PHSs in China.