Despite the necessity of using nurseries to raise young plants and trees prior to transplantation into the landscape, not enough is known about the impact of their associated climate on the growth and development of seedlings from initial germination through to transplantation and beyond. Furthermore, the effect of nursery environment on trait interactions and age-age correlations and their subsequent relation to traits in mature trees is of significant importance and interest to forestry practitioners but requires long-term experimental trials measured for multiple traits in multiple years. A multisite progeny-provenance trial of the economically and ecologically important species, Scots pine, was established in three environmentally distinct nurseries in Scotland and measured for traits relating to survival, growth, form and phenology while in the nurseries. Temperature variation and photoperiod were the only uncontrolled environmental variables during this period, and their effect on measured traits was found to be significant among nurseries from the first growing season onwards. Furthermore, interactions among traits were not always consistent among the different nurseries indicating that the use of proxy traits to enable selection of desirable traits may be more or less successful depending on the environment the trees are measured in. This study represents the first in a series examining trait variation in Scots pine from seedlings to mature trees, and highlights the importance of carefully considering the nursery environment when growing trees for transplantation.