Free plant growth-promoting bacteria in soil bioamendments (SBA) are easily outnumbered by competitors and predators in agricultural soils. Microencapsulation of the bacteria is an effective technique that provides a suitable microenvironment for their survival. In this study, we attempted to prepare poly(E-caprolactone) (PCL) microcapsules enclosing lactic acid bacteria (LAB), a plant growth-promoting bacteria, using the solvent-evaporation method via water-in-oil-in-water (W/O/W) emulsion. Three preparation parameters in the emulsion system were optimized based on the lactic acid production activity of the encapsulated LAB. A sodium alginate aqueous solution suspending the bacteria, a dichloromethane solution with dissolved PCL, and a poly(vinyl alcohol) aqueous solution were used as the inner aqueous phase (W), the oil phase (0), and the outer aqueous phase (W-o), respectively. Suitable volume ratio of W-i to O, concentration of sodium alginate in W-i, and the molecular weight of PCL in O were 0.1, 1.0%, and 40 kDa, respectively. The lactic acid production activity of the microcapsules prepared under the optimized conditions was approximately nine times higher than that of commercial SBA. Application to soil demonstrated that the microcapsules are effective in the removal of the root-knot nematodes.