Climate change is disrupting historical patterns of adaptation in temperate and boreal tree species, causing local populations to become maladapted. Tree improvement programs typically utilise local base populations and manage adaptation using geographically defined breeding zones. As climates shift, breeding zones are no longer optimal seed deployment zones because base populations are becoming dissociated from their historical climatic optima. In response, climate-based seed transfer (CBST) policies incorporating assisted gene flow (AGF) are being adopted to pre-emptively match reforestation seedlots with future climates, but their implementation requires accurate knowledge of genetic variation in climatically adaptive traits. Here we use lodgepole pine as a case study to evaluate the effects of selective conifer breeding on adaptive traits and their climatic associations to inform CBST and AGF prescriptions. Our approach compared 105 natural stand and 20 selectively bred lodgepole pine seedlots from Alberta and British Columbia grown in a common garden of 2200 seedlings. The effects of selection on phenotypic variation and climatic associations among breeding zones were assessed for growth, phenology and cold hardiness. We found substantial differences between natural and selected seedlings in growth traits, but timing of growth initiation was unaffected, growth cessation was delayed slightly (average 4 days, range 0.7 days to 10 days), and cold injury was slightly greater (average 2.5%, range 7% to 11%) in selected seedlings. Phenotypic differentiation among breeding zones and climatic clines were stronger for all traits in selected seedlings. Height gains resulted from both increased growth rate and delayed growth cessation, but negative indirect effects of selection on cold hardiness were weak. Selection, breeding and progeny testing combined have produced taller lodgepole pine seedlings that are not adaptively compromised relative to their natural seedling counterparts. Selective breeding produces genotypes that achieve increased height growth and maintain climate adaptation, rather than reconstituting genotypes similar to populations adapted to warmer climates. While CBST is needed to optimise seedlot deployment in new climates, an absence of systematic indirect selection effects on adaptive traits suggests natural and selected seedlots do not require separate AGF prescriptions.