The dataset is provided to support the analyses presented in, and to provide transparency for, the analyses performed in our paper entitled "The thyroid hormone metabolite Triac stimulates bone mineralisation in larval zebrafish", submitted to the Journal of Endocrinology. The dataset comprises the raw data, stored in CSV files, together with the R scripts used for data processing and analysis, as described in the Methods section. The dataset includes the complete set of experimental data underlying this study, comprising luciferase-based osteoblast activity assays, gene expression analyses (thyroid axis, calciotropic, osteoblast- and osteoclast-related genes), mineral content measurements, skeletal and craniofacial morphometry and cellular quantifications. Data were obtained from zebrafish across different developmental stages and exposure conditions.