In 1999, West Virginia University (WVU) established an organic farming systems project with a market garden section consisting of 32 plots measuring 16 × 25 ft arranged in a completely randomized design. Sixteen of these plots were managed as high-input and 16 as low-input plots. High-input plots received 10 tons/acre per year of dairy manure and a rye-vetch (Secale cereale and Vicia villosa) cover crop during each winter season since the inception of the experiment in 1999. Fertility in low-input plots was managed solely with an annual rye-vetch cover crop while both treatments also received 5 tons/acre of mixed species hay used as mulch in 2 of every 4 years. A 4-year rotation of crops, green bean (Phaseolus vulgaris), zucchini (Cucurbita pepo), tomato (Solanum lycopersicum), green pepper (Capsicum annuum), and lettuce (Lactuca sativa) in the Fabaceae, Cucurbitaceae, Solanaceae, and Asteraceae families, was established in 1999 and has been maintained ever since. Soil organic matter (SOM) in the upper 6 inches of the soil profile (4.4% in 1999) has remained unchanged in low-input plots at 5.2% in 2004 and 5.4% in 2014, the year following transition and most recent data collection, respectively. During this same time period, significant increases in SOM from 6.4% in 2004 to 8.7% in 2014 were observed in high-input plots. Bulk density was lower in high-input plots than low-input plots in 2014. Despite these improvements in soil quality, high-input plots showed very high levels of phosphorus and potassium. Over the duration of the experiment, yearly manure application increased yields by 22% in all crops combined; however, individual crops responded quite differently. The yield was 9%, 25%, 24%, and 24% higher in high-input plots than in low-input plots for tomato, pepper, zucchini, and green bean, respectively. Manure application in addition to green manures and hay mulch incorporation was found to result in significant economic returns.