Linseed oil is utilised in a broad range of industrial and food applications, which make desirable a thorough understanding of the factors that influence its yield and quality. In this study, we used a Bayesian hierarchical model to investigate the impact of genotype and climatic variables on linseed seed and oil yield, as well as fatty acid composition, by utilising a germplasm collection database. Data were collected for 25 years at two nearby locations in Northern Italy, covering between 192 and 252 cultivars. After model optimisation, the cultivar-specific intercept coefficient exhibited the highest degree of differentiation across cultivars for all the variables under investigation. The response to temperature showed on the other hand no difference among cultivars, but it was generally negative for seed yield and seed oil content while it did not impact on fatty acids except for reducing the ratio of polyunsaturated to saturated fats in a few cultivars. A higher variability was detected for the cultivar response to rainfall, which affected seed yield and oil content either negatively or positively. Rainfall also influenced fatty acid composition, in particular the fraction of monounsaturated acids which were negatively impacted in all cultivars. Overall, the seed yield was the variable most affected by weather factors, which accounted for a value ranging between −27.9 % and 14.9 % on the average characteristic value of the cultivar, whereas for all other variables, the deviation was always less than 8 % in absolute value. The study also analysed the effect of autumn sowing compared to spring sowing, more commonly practiced in the study sites. Autumn sowing increased seed yield by up to 79.4 %, whereas oil content rose by no more than 1.6 %. While the saturated and monounsaturated fractions of fatty acids decreased, the polyunsaturated fraction rose to a maximum of 13.1 %. The ratio of polyunsaturated to saturated fats was increased up to 29.4 %.