Little is known about the economics of small-scale beekeeping, due in part because many of these beekeepers are motivated by personal enjoyment and not profit. These beekeepers, however, represent more than 90% of US beekeeping population, so economic analysis of this majority group is warranted. Understanding how management practices impact colony profitability in small apiaries can inform beekeeper management decisions. Best management practices (BMPs) can increase colony productivity and survival, but often require additional labor and materials compared to less intensive beekeeping practices. Here, we investigate the impact of BMPs on the profitability of small-scale beekeeping. We found that BMPs required higher costs in labor and materials, but that they also produced higher revenue from honey and nucleus colony production. As a result, after three years, BMP apiaries were 8 times more profitable than less intensively managed apiaries. The increased profitability in BMP apiaries is largely attributed to improved colony health and survival due to more active Varroa management and reduced Varroa and viral loads. These results can inform small scale beekeeper budgeting and management, and also support extension efforts to increase BMP adoption.