Plant protection methods, even those considered as safe for the environment and consumers, may have unexpected effects on nontarget organisms. The effect of broad bean protection, using Pythium oligandrum, paraffin-coated garlic pulp, and extract from grapefruit seeds and pulp on the abundance of epigeic and soil arthropodofauna in a 3-year field experiment was estimated. The effect was compared with chemical protection, which served as the reference to the conventional system. Use of nonchemical products did not affect the overall abundance of the studied arthropods such as Arachnida (except Acarina), Carabidae, Staphylinidae, and Collembola. These methods, however, may favor Formicidae. In comparison to chemicals (carboxin, mancozeb, deltamethrin, and alpha-cypermethrin), nonchemical preparations seemed to be safer for soil mites—they limited their abundance to a lesser degree. Some individual carabid species showed differing responses to the applied protection methods: Amara aenea occurred only in nonchemically protected areas, Platynus assimilis tends to prefer broad beans protected solely with P. oligandrum, while Anchomenus dorsalis prefer plots protected chemically (seed treatment and 3-time spraying). This may be the effect of the different shading of the soil surface as a result of the influence of protection measures on plant growth. Other explanations may include different vulnerability of species to preparations as well as indirect reaction to the occurrence of other taxa (reduced competition and impairment of food sources) or hormesis.