Soil testing strategies that include biologically based indicators in organic and alternative farming systems are needed in order to improve recommendations that balance production and environmental goals. In this study, soil samples were collected before and after soils were transitioned from conventional row crop production to organic management using rotations that varied in both their inputs and tillage intensity. Ley-, row crop- and vegetable-based farming systems were implemented using locally specific production practices. Subplots were imposed within each system to allow comparison of farming systems without amendment and with dairy manure- and compost-amendment. Soil analyses included standard chemical tests (0–15 cm) for available phosphorus, exchangeable potassium, calcium, magnesium, pH, total organic carbon (SOC) and total nitrogen (TN). Biological assays (0–15 and 15–30 cm) included particulate organic matter-C and -N (POM-C, POM-N), soil and POM C:N ratios, fluorescein diacetate (FDA) hydrolysis, potentially mineralizable N (PMN) and hydrolysable amino-N + NH4 (IL-N). Even though cropping and tillage intensity varied among systems (ley < row crop < vegetable), organic matter and nutrient reserves were not statistically different. Nutrient concentrations tested medium to high, even without compost or manure application. Labile fractions of soil organic matter were more enriched in the deeper sampling depth; whereby, POM stocks within the 15–30 cm depth increased by 20% on average compared to roughly 6% in the surface depth. This and observed changes in other properties demonstrate the multiple benefits derived from use of winter annual or perennial crops. Results from our analyses suggested PMN and POM have particular promise as metrics of change in commercial soil testing facilities to assist recommendations for amendments to balance production and environmental goals.