Strategies aimed at achieving food safety in crops of high nutritional value should be carried out through sustainable agricultural practices aimed at soil conservation, high yield and food safety. This latter characteristic implies food production without detectable traces of agrochemicals that threaten health. The objective of this study was to assess the effect of the herbicide glyphosate on the chemical and biological fertility of the soil and to determine its residual activity on biofortified bean seeds in Codazzi, Department of Cesar, Colombia. The method included a correlational analysis of soil quality, crop yield and residuality in bean grains. The treatments included glyphosate application and synthetic and natural mulches, compared to manual control. The results showed differences in the response of chemical, microbiological and yield indicators between treatments and the initial conditions of the bean rhizosphere. The use of the herbicide glyphosate in mulch-free soil generates yield losses of 29% associated with a higher incidence of pests and fungal diseases; in all treatments, no glyphosate residuality was detected in seeds; however, residuality was detected in other molecules derived from insecticides associated with the local production system. In conclusion, in plots with high weed pressure by Cyperus rotundus, the use of mulch is recommended as an alternative to maintain bean productivity over time; by offering protection against the effect of the herbicide on both the root system of the plant and the soil microbiota of the biofortified bean crop.