Herbicides are commonly used to control weed. However, some plants are resistant to such products. To identify less harmful herbicides, it is crucial to search for different mechanisms of action. Thymol is an easily acquired allelopathic compound, capable of producing its respective semisynthetic derivative, thymoxyacetic acid. The aim of this study was to determine the effects of thymol and thymoxyacetic acid molecules as bioherbicides in greenhouse at the concentration of 3 mmol L −1 in pre- and postemergence applications in five species: Amaranthus viridis L., Cucumis sativus L., Lactuca sativa L., Eleusine indica L., and Sorghum bicolor L. The initial seedling development and DNA changes were analyzed. These molecules were contrasting with the solvent, in the negative control, and with the glyphosate, in the positive control, promoting phytogenotoxic activities. The toxic effect of thymoxyacetic acid was more effective in preemergence and thymol’s in postemergence. We also observed a reduction in the germination speed index and root growth with a negative correlation to the increase in potassium leaching. Damage to the root and shoot of the seedlings was verified at the DNA level, and the phytotoxicity of the plants treated with the herbicide glyphosate was similar to the plants treated with the natural molecules tested. The bioherbicidal effect of thymol and thymoxyacetic acid exacerbates the reduction of the environmental impact caused by the disordered and increased use of residual pesticides.