This cross-sectional observational study aimed to identify prepartum management, environmental, and animal factors associated with clinical –lameness, metritis, mastitis– and subclinical –calcium imbalance, magnesium imbalance– diseases in pasture-based dairy cows. A total of 565 cows from 25 commercial dairy farms in southern Chile were enrolled over four months. Data on prepartum management and environmental conditions were obtained through a survey and inspections of prepartum paddocks. Cows were evaluated two times. In the first evaluation, between 30 to 3 days before calving, cows were assessed for lameness, body condition score, and blood samples were collected to measure nonesterified fatty acid (NEFA), calcium (Ca), and magnesium (Mg). In the second evaluation, between 3 to 21 DIM, cows were assessed for metritis, lameness, and blood samples were collected and analyzed for total Ca and Mg concentration. Cows were considered as having Ca imbalance if Ca < 2.0 mmol/L, and Mg imbalance if Mg < 0.65 mmol/L. Postpartum clinical mastitis was diagnosed based on the foremilk's daily condition and udder assessed by the milker at each milking during the postpartum transition period. Multivariable logistic regression models, controlling for the farm as a random effect, were built to identify prepartum factors for each postpartum disease. The odds of postpartum lameness were higher for cows that were lame during the prepartum period, had elevated prepartum NEFA concentrations, had greater parity, and for cows that were kept in paddocks with no grass cover. The odds of metritis were higher in cows with lower parity, with increased prepartum NEFA, in cows that had dystocia, and farms with predominantly Holstein breed, and that did not have calving records. The odds of clinical mastitis were higher for cows lame during the prepartum period. The odds of Ca imbalance were higher in cows with a long dry period, dystocic calving, and in farms without prepartum anionic salts supplementation. The odds of Mg imbalance were higher in cows with lower prepartum Mg concentrations, higher prepartum Ca concentration, and higher parity. Our findings indicate that farmers could benefit from refining these areas to improve their cows’ health and welfare.