Recently, numerous novel putative biomarkers of food intake (BFIs) have been discovered to complement self-reported dietary assessment. However, few BFIs have been properly validated for their intended applications due to lack of comprehensive validation frameworks, need for complementary expertise and scattered data in the literature. Although a few biomarker validation frameworks have been proposed, they still require improvement to fully encompass relevant criteria and provide precise guidance for harmonized evaluation of BFI validity. The FoodPhyt consortium developed a new scoring system based on the FoodBAll validation scheme, to standardize scoring and allow comparison of BFIs with varying validity. The following criteria were included: level of identification and plausibility (pass-or-fail criteria), specificity, variability in plants/foods and biological samples, dose-response, robustness, and analytical characterization. The score is bipartite and includes availability of supporting literature (data availability), and BFI quality (performance). Data availability helps assessing confidence in the assigned score, while highlighting knowledge gaps. Detailed guidelines and examples are provided to facilitate BFI scoring and reproducible application. An online repository, BFI-Hub (https://biomarker.plantintake.eu/app/), was developed to share validity scores of BFIs and detailed validation data. This database represents a key step to make BFI information universally accessible and facilitate application of BFIs in practice.