Honey bees (Apis mellifera L.) are critical to the pollination of many important crops in the United States, and one crop that demands large numbers of colonies early each year is almonds. To provide adequate numbers of colonies for almond pollination, many beekeepers move colonies of bees to high-density holding yards in California in late fall, where the bees can fly and forage, but little natural pollen and nectar is available. In recent years, high colony losses have occurred in some operations following this management strategy, and alternative approaches, including indoor storage of colonies, have become more commonly used. The current study evaluated colonies kept indoors (refrigerated and/or controlled atmosphere) for the winter compared with those kept outdoors in either Washington or California. Colonies were evaluated for strength (frames of bees), brood area, lipid composition of worker bees, colony weight and survival, parasitic mites (Varroa mites, tracheal mites), and pathogens (Nosema spp.). No differences were found in colony weight, survival, parasitic mite levels, or pathogen prevalence among the treatments. Colonies stored indoors and outdoors in WA had significantly more frames of bees and less brood present after the storage period than colonies stored outdoors in CA. Lipid composition of honey bees stored indoors was significantly higher than colonies stored outdoors in WA or CA. The implications of these findings for overall colony health and improved pollination activity are discussed.