Summary Orobanche species (broomrapes) are parasitic weeds which dramatically decrease the yields of many economically important dicotyledonous crops, including pea (Pisum sativum), in Mediterranean areas. Previously, we identified some Rhizobium leguminosarum strains, including P.SOM, which could both promote pea development and significantly reduce infection by Orobanche crenata, notably through induction of necrosis of attached parasites. In the present study, induced resistance against broomrape in the nodulated pea was shown to be associated with significant changes in rates of oxidative lipoxygenase (Lox) and phenylpropanoid/isoflavonoid pathways and in accumulation of derived toxins, including phenolics and pisatin (pea phytoalexin). Changes were followed for 5 weeks after inoculation and attack by Orobanche. In contrast to non‐inoculated plants or Orobanche only infected plants, polyphenoloxidase (PPO) activity and hydrogen peroxide content increased in response to bacteria inoculation indicating the involvement of oxidative processes. In parallel, the nodulated roots displayed high Lox activity related to the overexpression of the lox1 gene. Similarly, the expression of phenylalanine ammonia lyase (PAL) and 6a‐hydroxymaackiain 3‐O‐methyltransferase (Hmm6a) genes were induced early during nodule development, suggesting the central role of the phenylpropanoid/isoflavonoid pathways in the elicited defence. As a consequence, the derived products, phenolics and pisatin, accumulated in response to rhizobacteria and conferred mechanical and chemical barriers to the invading parasite. These results highlight the likely role of signalling pathways in induced resistance and suggest these mechanisms should be enhanced through integrated Orobanche management practices.