Production of fruits and vegetables provides nutrient dense and high value crops. However, horticulture production is often very intensive and degrading to soil, with high levels of soil disturbance, high use of fertilizer inputs, and with prolonged periods of exposed soil. This can lead to increased soil degradation when compared to other types of cropping. We used a subset of the Atlantic Soil Health Laboratory’s database of on-farm soil samples collected between 2016 and 2018 to assess the impact of cover crop (CC) use in horticulture production in Nova Scotia on soil health. We analyzed 21 soil health parameters on soil collected from 14 fields, seven of which incorporated CCs in their crop rotation and seven of which used no CCs. The inclusion of CCs significantly increased permanganate oxidizable carbon (POX), soil respiration, autoclaved-citrate extractable (ACE) protein, residual soil nitrogen (N), and biologically available N. However, we also found that the variation in these parameters was greater when CCs were part of the rotation. This is likely attributable to the wide range of CC species used and differences in their management, such as the chosen termination method. While cover cropping is seen as a best management practice to improve soil health, simply using a CC in a horticulture rotation does not necessarily lead to improved soil health. Research trials on specific CC species and management to target soil degradation are needed to tailor recommendations to ensure the desired soil health outcomes can be achieved with CC use.