Conventional intensive farming systems can result in degraded soil. It is therefore important to monitor this effect periodically by delineating management zones (MZ) based on soil quality indices (SQI) in order to maintain and improve the soil characteristics in a precision farming environment and obtain homogeneous rice yields. The aim of this study was to determine and spatialise SQI and delineate MZ for cultivating flooded rice in an area of Fluvisols in Huila, Colombia. Forty-one georeferenced soil samples were collected from the 0 to 20 cm layer, and the physical, chemical and biological attributes of the soil were analysed to calculate the Integrated Quality Index (IQI) and the Nemoro Quality Index (NQI) using linear scoring functions. Geostatistical tools were then used to fit semivariogram models of the SQI, and interpolated using ordinary kriging to map the MZ using the QGIS software. The IQI and NQI showed a moderate spatial correlation, which allowed three distinct MZ to be identified and delineated. Attributes, such as bulk density (Bd), total porosity (TP), soil respiration (SR), available water (AW) and soil organic matter (SOM) were significant and can be used as a guide by farmers for restoring the quality of the soil in rice production. The method proved to be effective, and provided an information base to be used in the local management of areas of rice cultivation in the study region.