This study describes the time-course of the accumulation of total soluble proteins (TSPs) and vegetative storage proteins (VSPs) and of the transcripts of cold-inducible (CI) and VSP-encoding genes in taproots of two alfalfa cultivars (AC Caribou and Europe) during their acclimation to natural autumn hardening and overwintering conditions in eastern Canada. The impact of a defoliation in September on these winter hardening-related changes was also assessed. Both concentrations and pools of VSPs increased significantly between early September and mid-October and remained unchanged thereafter, concomitantly with the disappearance of VSP-encoding transcripts. Other soluble protein constituents continued to increase later in the autumn and early winter and accounted for nearly 60% of taproot TSP pools in winter. As a result, VSP abundance relative to TSPs decreased markedly during the winter. The increase in the levels of CI transcripts was induced by lowering temperatures, and distinct patterns suggest differences in the regulation of their accumulation. RNA analyses revealed that the accumulation of VSP transcripts during the autumn precedes the accumulation of CI transcripts. Autumn defoliation interrupted the accumulation of both TSPs and VSPs during autumn hardening and repressed the transcript levels of two CI genes differentially between cultivars. The well-documented impact of autumn defoliation on the vigour of spring regrowth and long-term persistence of alfalfa could be related to its negative impact on the accumulation of VSPs and TSPs and on the expression of genes encoding CI proteins potentially involved in cold tolerance and pathogen resistance.