Anthropogenic activities impact soil in varying degrees, from preserving natural landscapes to intensive agriculture which among the farm practices that impact the soil are the cropping systems. Information on cropping systems and soil impacts in northern territories is still missing. This study assesses the effect of different cropping systems on soil health -physical, chemical and biological soil properties and indicators of soil health - at the Lakehead Agricultural Research Station [LUARS] in northern Ontario, Canada. The study compares three cropping systems (perennial crops-pasture, grass, and annual crops -wheat, barley, corn, soybeans) and two forest areas (conifer plantation and naturally regenerating mixed wood forest) at LUARS. Soil samples were collected at different depths and analyzed for various indicators using the Cornell Soil Health Assessment framework. The results showed the soil health scores varied among cropping systems, with natural forest and perennial crops-pasture having higher scores compared to annual crops -wheat, barley, corn, soybeans. Soil organic matter was found to be lowest in annual crops -wheat, barley, corn, soybeans, while aggregate stability was highest in natural forests. The study also identifies the soil health gap, which represents the difference between the health of a particular cropping system and a benchmark. The soil health gap analysis can help farmers implement practices to improve soil health and increase the resilience and sustainability of agroecosystems. Overall, this study emphasizes the importance of understanding the effect of cropping systems on soil health and provides insights into potential strategies for improving farm practices.