Soil enzymes activities can be used to measures of microbial activity, soil productivity, soil ecology and fertility. Soil enzyme and microbial activities act as the indicators of soil health. The objectives of this study were to examine the influence of liquid organic biofertilizer and sprout extract on soil enzyme and microbial activities and their effect in shallot yield. The experimental design was completely randomized block design with three different treatments as following liquid organic biofertilizer (LOB), sprout extract (SE), and mixed of liquid organic fertilizer and sprout extract. The result showed that treatment of LOB gave the highest activity of phosphomonoesterase and urease measured, and followed by SE, LOB+SE and control. The LOB treatment showed the highest microbial respiration as also indicated in the highest population number of total bacteria. However, LOB + SE treatment gave the highest number of IAA producing bacteria as well as the yield of shallot. Therefore, it is confirmed from this work that application of liquid organic biofertilizer and sprout extract potentially could increase soil enzyme activities, microbial population number and the yield of shallot.