Enzymes involved in the breakdown of cellulose and hemicellulose showed maximum activities in plots amended with manure. Conversely, the enzymes involved in the hydrolysis of starch and phosphate esters peaked under mineral N fertilization. Linear regression analysis indicated close associations between enzyme activities and other fundamental soil properties related to soil quality, and principal component analysis separated the soil samples according to their responses to organic and mineral N fertilization. We conclude that microplate-scale fluorimetry is a fast throughput tool for the measurement of multiple soil enzyme activities as soil quality indicators.