Use of organic fertilizers is one of the solutions to mitigate soil health deterioration, but it often promotes outbreaks of insect pests in soils. However, organically fertilized crops may also contain higher concentrations of defensive secondary metabolites than those grown with conventional inorganic fertilizers. Therefore, interactions between crops and insect pests in soils may change due to fertilizer type. To understand these complex interactions, we grew Nozawana (Brassica rapa var. hakabura) while independently manipulating fertilizer type (inorganic or organic fertilizer) and magnesium lime (use or no use). Yield, glucosinolates (GSLs) levels, and vitamin C concentration in Nozawana, as well as soil chemical properties and arthropod abundance in the field were investigated. Shoot fresh weight was 3.9 kg/m2 under the organic fertilizer condition whereas 4.3-4.5kg/m2 under the other conditions. Nozawana grown with organic fertilizer contained more aliphatic GSLs, which can act as defensive chemicals against insect pests. The magnesium lime application offset the difference of aliphatic GSLs between organic and inorganic fertilizer. The use of organic fertilizers increased the abundance of the insect pest Delia platura. Indole GSL concentrations in taproots was the highest under the inorganic fertilizer condition. Because indole GSLs are induced by root herbivory, this may suggest that D. platura feeding was the most severe when inorganic fertilizer was applied.