For over a decade, high percentages of honey bee colonies have been perishing during the winter creating economic hardship to beekeepers and growers of early-season crops requiring pollination. A way to reduce colony losses might be moving hives into cold storage facilities for the winter. We explored factors that could affect the size and survival of colonies overwintered in cold storage and then used for almond pollination. The factors were when hives were put into cold storage and their location prior to overwintering. We found that colonies summered in North Dakota, USA and moved to cold storage in October were larger after cold storage and almond pollination than those moved in November. Colony location prior to overwintering also affected size and survival. Colonies summered in southern Texas, USA and moved to cold storage in November were smaller after cold storage and almond pollination than those from North Dakota. The colonies also were smaller than those overwintered in Texas apiaries. Fat body metrics of bees entering cold storage differed between summer locations. North Dakota bees had higher lipid and lower protein concentrations than Texas bees. While in cold storage, fat bodies gained weight, protein concentrations increased, and lipids decreased. The decrease in lipid concentrations was correlated with the amount of brood reared while colonies were in cold storage. Our study indicates that in northern latitudes, overwintering survival might be affected by when colonies are put into cold storage and that colonies summered in southern latitudes should be overwintered there.