This dataset contains phenotypic data on Scots pine cones and seeds sampled from individual trees in a long-term common garden trial. For each tree, overall cone counts were conducted and five cones were sampled in February 2024. Seventeen phenotypic traits were measured for each cone between June and July 2024. Traits include cone length, cone width, cone dry weight, scale length, scale width, scale count, stalk length, profile and colour, seed number and mean seed weight. Full details about this dataset can be found at https://doi.org/10.5285/b98e92cf-6ff5-42e2-8053-021ea04db01c