Increasing atmospheric CO₂ and other greenhouse gases are drivers of global climate change. Soil carbon sequestration has been proposed as a means to mitigate atmospheric CO₂ and the effects of climate change. Soil microorganisms play a key role in soil C cycling. Recent studies have shown that deeper layers of soil are more dynamic in carbon cycling than previously thought. The objective of this research was to assess the effect of tillage and N source on deep soil organic carbon (SOC) stocks, C stability and microbial community structure. The soil was a Kennebec silt loam previously planted with C₃ crops prior to cultivation of continuous corn (Zea mays L.) established in 1990. The experiment was a split-block design with main treatments of conventional tillage (CT) and no-till (NT) and subtreatments of organic fertilizer (OF) and mineral fertilizer (MF). Samples were collected to a depth of 1.2 m. Measurements included SOC, dissolved organic carbon (DOC) and microbial community using phospholipid fatty acid (PLFA) analysis. Source and stability of carbon was measured using δ¹³C in soil and CO₂ during an incubation experiment.