Fixed and broad screening intervals for drug-drug interaction (DDI) alerts lead to false positive alerts, thereby contributing to alert fatigue among healthcare professionals. Hence, we aimed to investigate the impact of customized screening intervals on the daily incidence of DDI alerts. An interrupted time series analysis was performed at the University Hospitals Leuven to evaluate the impact of a pragmatic intervention on the daily incidence of DDI alerts per 100 prescriptions. The study period encompassed 100 randomly selected days between April 2021 and December 2022. Preceding the intervention, a fixed and broad screening interval of 7 days before and after prescribing an interacting drug was applied. The intervention involved implementing customized screening intervals for a subset of highly prevalent or clinically relevant DDIs into the hospital information system. Additionally, the sensitivity of the tailored approach was evaluated. During the study period, a mean of 5731 (± 2909) new prescriptions per day was generated. The daily incidence of DDI alerts significantly decreased from 9.8% (95% confidence interval (CI) 8.4;11.1) before the intervention, to 6.3% (95% CI 5.4;7.2) afterwards, p < 0.0001. This corresponded to avoiding 201 (0.035*5731) false positive DDI alerts per day. Sensitivity was not compromised by our intervention. Defining and implementing customized screening intervals was feasible and effective in reducing the DDI alert burden without compromising sensitivity.