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.