Ammonia-oxidation is the first rate-limiting step of the nitrification process performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). The response of ammonia oxidizers to agricultural management determines the forms of nitrogen available for plant nutrition and the potential for nitrate leaching, nitrous oxide emissions, and soil acidification. We investigated the potential nitrification rates (PNR) of AOA and AOB through the use of a specific inhibitor of bacterial nitrification, and the amoA gene abundance of AOB and AOA under potato, fallow and eucalyptus land uses in an agricultural system in the Central Andes of Bolivia. AOA dominated PNR and amoA gene abundance under all land uses. The ratio of AOA to AOB abundance decreased with soil pH, due to higher AOB abundances under the less acid soils of potato crops. Eucalyptus led to reduced AOB amoA abundances and PNR of both AOA and AOB, while PNR were highest under potato soils, and the contribution of AOB to total PNR increased. Specific PNR, as expressed per amoA gene copy numbers, was 12, 14 and 62 times higher for AOB than for AOA in potato, fallow and eucalyptus soils, respectively. AOB and AOA PNR were positively related to their respective amoA gene copy numbers, but for AOA the relationship depended on land use. This study demonstrates the interest for measuring separately nitrification rates of AOA and AOB for a mechanistic understanding of nitrification in different environments, as well as the importance of measuring process rates for assessing the environmental consequences of land use management.