While cover crops (CC) are known to enhance soil health, outcomes are often subtle and confined to a shallow surface soil layer. We assessed 15 soil health indicators over three CC trials with a 15-species Blend polyculture, a Mustard biculture (white (Sinapsis alba L.) and brown (Brassica juncea (L.) Czern.) mustards), Buckwheat (Fagopyrum esculentum Moench), and Faba bean (Vicia faba L.) monocultures, and a Weedy fallow (no CC, weeds allowed to grow) on an organic farm in southern Alberta. Soil sampling times included (i) summer pretermination; (ii) fall post-termination; and (iii) spring post-termination of CC. Twelve of 15 soil health indicators showed significant effects of CC treatment for at least one sampling time. Soil organic C (SOC) ranked highest with 80% of sampling times showing significant CC effects. N-related indicators (total N (TN), nitrate-N)) were also quite sensitive, being significantly affected by CC treatment at 60% of sampling times. Three soil health indicators (acid phosphomonoesterase (AcP), wet aggregate stability, and free-living nematodes (FLN)) were consistent in their nonresponses to CC treatment at all sampling times. Comparing CC treatments with a Weedy fallow, showed that not all enhancements of soil health were explained by inclusion of a CC, with Weedy fallow as effective for some indicators. A polyculture Blend significantly enhanced soil health over a monoculture CC or Weedy fallow in 46% of instances of soil health indicator improvement. While CC led to enhancement of soil health, results were not always consistent, being contingent on specific indicators.