The effectiveness of pesticide reduction policies in the European Union (EU) depends critically on robust, scientifically grounded indicators that can reliably monitor pesticide-related risks across Member States. The Pesticide Load Indicator (PLI), developed in Denmark in the 2000s, offers a transparent and policy-relevant framework for assessing pesticide risk. Although it has successfully supported Denmark’s national strategies for over a decade and is drawing attention in other EU countries, several methodological limitations hinder its broader applicability. This letter identifies five such limitations and proposes corresponding updates to enhance the indicator’s scientific robustness and scalability across the EU: (1) consistent hazard assessment across compartments, (2) precautionary treatment of missing data, (3) updated hazard metric selection, (4) harmonised normalisation procedures and (5) a statistically grounded weighting protocol. These methodological updates aim to establish a harmonised PLI suitable for EU-wide policy applications, such as fiscal instruments (e.g. differentiated taxation based on hazard levels) and pesticide risk assessments.