Current agricultural practices are unsustainable due to their harm to the environment and soil health. Soil organic matter (SOM) is critical to maintaining healthy soils and productivity. However, SOM loss can be accelerated through agricultural management practices such as tillage. Conservation practices such as no-till (NT) and cover crops (CC) can potentially mitigate these negative consequences of conventional agriculture management and enhance soil health. While this may be true, the positive effect of these conservation practices has been inconsistent, as SOM status is affected by a variety of soil management practices. An additional challenge is that many metrics of soil health change very slowly, making management recommendations difficult in the short-term. Therefore, certain indicators have been developed to be more sensitive and responsive to management practices. Presently, little research has looked at the combined, or stacked, effect of using both reduced tillage system and cover crops at the same time. The primary objective of this study is to investigate the short-term effects of tillage systems and cover crop on different aspects of soil health that include: (1) agronomic and economic returns, (2) soil chemical and biological health indicators and water quality, and (3) soil physical health indicators. This study was established in the fall of 2017 through the fall of 2019. The experimental design was a split-split plot design with tillage system as the main treatment and cover crop as the sub-treatment in a corn (Zea mays L.)–soybean [Glycine max (L.) Merr.] rotation. Cover crop treatments were no cover crop (NC) and winter rye (Secale cereale L.) cover crop (CC). Tillage treatments were chisel plow (CP) and no-till (NT). Each treatment combination was executed in this 2x2 complete factorial design. Soil samples were taken in the spring and fall of each year and analyzed for the different parameters within the above objectives. A secondary objective was to evaluate the effect of soybean residue quality in the two different tillage systems by measuring decomposition in situ of three different soybean varieties with C:N ratios ranging from 29:1 to 47:1. All significant effects were main effects; interaction effects were not observed with tillage and cover crop treatments. The findings of this study suggest that CP decreases soil moisture and increases soil temperature. Soil daily maximum temperature was 2.4℃ lower in corn and 4.5℃ lower in soybeans for NT compared to CP, and soil moisture was 8.8% greater in corn and 8.3% greater in soybeans with NT. Aboveground CC biomass was an average of 34% lower in NT than CP. The results also showed an increase in yield in the first year of CC in corn and the second year of CC treatment in soybean yield (9.7% and 3.9%, respectively) compared to NC treatment. Economically, input costs were $65 ha-1 lower with NT compared to CP, and $83 ha-1 higher with CC than NC. When the use of CC improved yield, economic returns increased by an average of $11 ha-1 before accounting for cost-share programs valued at $80 ha-1. Soil total organic C pools and pH were less responsive to the treatments, but more sensitive indicators such as MBC and ρb showed improvements over the course of two years associated with NT and CC. MBC was greater in NT compared to CP in corn plots and increased 52% in CP–CC than the other treatments in soybeans in the spring of 2019. In the spring of 2019, ρb was 8% lower in CC than NC in corn plots. The conservation practices of NT-CC showed improvements to water quality by reducing nitrate leaching by 20% with tillage and 9% with CC, and improvement of water infiltration. Additionally, NT had faster and greater soybean residue decomposition, regardless of C:N ratio. In conclusion, when NT and CC are managed properly in cool wet soils in North Central Iowa, they can produce competitive yields and economic returns while improving soil health and water quality. These findings are important because optimal systems approaches are necessary to meet the major challenges facing farmers. This research represents a step in the process of combating the lack of research in systems approaches towards solutions to these challenges. The integration of cover crops and reduced tillage as potential solutions are strengthened by finding no evidence of certain perceived barriers to adoption, namely yield penalties caused by wet soils and nutrient deficits due to cover crops.