Abstract Background During the COVID-19 pandemic hospitals reorganized their resources and delivery of care, which may have affected the number of healthcare-associated infections (HAIs). We aimed to quantify changes in trends in the number of HAIs in Dutch hospitals during the COVID-19 pandemic. Methods National surveillance data from 2016 to 2020 on the prevalence of HAIs measured by point prevalence surveys, and the incidence of surgical site infections (SSIs) and catheter-related bloodstream infections (CRBSIs) were used to compare rates between the pre-pandemic (2016–February 2020) and pandemic (March 2020–December 2020) period. Results The total HAI prevalence among hospitalised patients was higher during the pandemic period (7.4%) compared to pre-pandemic period (6.4%), mainly because of an increase in ventilator-associated pneumonia (VAP), gastro-intestinal infections (GIs) and central nervous system (CNS) infections. No differences in SSI rates were observed during the pandemic, except for a decrease after colorectal surgeries (6.3% (95%-CI 6.0–6.6%) pre-pandemic versus 4.4% (95%-CI 3.9–5.0%) pandemic). The observed CRBSI incidence in the pandemic period (4.0/1,000 CVC days (95%-CI 3.2–4.9)) was significantly higher than predicted based on pre-pandemic trends (1.4/1000 (95%-CI 1.0–2.1)), and was increased in both COVID-19 patients and non-COVID-19 patients at the intensive care unit (ICU). Conclusions Rates of CRBSIs, VAPs, GIs and CNS infections among hospitalised patients increased during the first year of the pandemic. Higher CRBSI rates were observed in both COVID-19 and non-COVID-19 ICU population. The full scope and influencing factors of the pandemic on HAIs needs to be studied in further detail.