This research concern the characterization of the rhizosphere bacterial community from pea (sole- and intercropping), wheat (sole- and intercropping), and from bare soil. The samples were obtained from two independent field experiments. Both experiments were performed at the Experimental Unit INRAE-Epoisses, France (47°14′11.2″ N 5°05′56.1″ E), the first from October 2016 to July 2017 (sampling in May 2017), the second from October 2017 to July 2018 (sampling in May 2018). The goal of the study was to evaluate the impact of the pea-wheat intercropping of different wheat and pea cultivars on bacterial rhizosphere communities as characterized by their biodiversity, structure and co-occurrence networks. Samples ‘BP’ belong to the first experiment, samples ‘QA’ belong to the second one. Moreover, samples ‘QA.60’, ‘QA.61’, ‘QA.125’, ‘QA.126’, ‘QA.186’, ‘QA.187’, ‘QA.188’, ‘QA.189’, ‘QA.190’, ‘QA.191’, ‘QA.192’ and ‘QA.193’ belong to bare soil.