Using food composition data from multiple countries requires a high level of harmonization between datasets, at food, component, and value documentation level. To achieve this, nutrient values in European food composition databases were documented using EuroFIR guidelines and thesauri. Our aims were to evaluate the impact of harmonized documentation of macronutrients and usefulness for research and/or policy. Data on 28,914 foods and 292,240 macronutrient values from 26 European food composition datasets were extracted from the FoodEXplorer™ web-based tool for simultaneously searching and comparing food composition data. Documentation on most properties describing the nutrient values was complete, however the percentage coded as unknown varied from 14% to 49% for value type, method type, method indicator and acquisition type. Some inconsistencies were found in coding, and documentation on references was incomplete (about 65% missing information). The harmonized manner of data documentation using the EuroFIR guidelines for food, component and value documentation, allows for data exchange. However, comparability of carbohydrate, dietary fiber, protein and energy values remained difficult due to multiple definitions and formulas used or due to lack of details on analytical and calculation methods. Therefore, data on these components cannot be regarded as fully comparable in Europe without further harmonization; care should be taken when using these data for multiple country comparisons. To achieve further comparability within the FoodEXplorer™ tool, information on methods and references used should be completed for each dataset and energy, carbohydrate and protein values should be recalculated in a uniform way. This remains a major challenge for most countries, but is urgently needed.