Intensive dairy production in southern Idaho is associated with the annual application of manure to croplands. However, a one‐time heavy application of manure could alternatively be used as a means to improve soil fertility and health for years or even decades, circumventing the need for frequent applications. To determine if this practice would negatively affect soil properties in the short term, we analyzed chemical and biological indicators of soil health for 2 years after dairy manure incorporation. Soil indicators measured were pH, electrical conductivity, extractable nitrogen (N) and phosphorus, total carbon (C) and N, enzyme activities, net N mineralization, soil organic C, soil protein, active C, ammonia oxidation potential, and particulate organic matter. Manure (with and without synthetic fertilizer) was found to significantly affect chemical and biological indicators in both topsoil (0–15 cm) and subsoil (15–30 cm), but the responses were greater in the subsoil. This can be attributed to the fact that manure was incorporated to approximately 30 cm via moldboard plow. All indicators responded positively to manure, except pH, which decreased slightly in the subsoil in the first year after application. Principal component analysis of chemical and biological indicators, across all years and depths, showed that the first two components explained 62% and 8.5% of the variance. While soil indicators were not adversely affected by manure, silage corn (Zea mays L.) yields in year 1 were significantly lower in manured plots, though in year 2, barley grain (Hordeum vulgare L.) yields were statistically similar among manure and fertilizer.