Updated version of the dataset used in the article “Methane emissions in pasture-based dairy systems with contrasting intensification strategies in Uruguay in two periods: operational simplicity vs maximised productivity”, published in Animal – Open Space journal. The file contains two sheets: Metadata_paper ANOPES-D25-00065: Includes individual cow records for all measurements across two periods and the two pasture-based dairy systems (operational simplicity – OS – and high productivity – HP). Each row represents one cow on one sampling date and contains information on methane emissions, milk production traits, and animal characteristics. Variables description: Provides detailed definitions and units (or types) for all variables included in the dataset.