In order to evaluate the quali-quantitative traits of fennel (Foeniculum vulgare L.) when intercropped with common bean (Phaseolus vulgaris L.) in different cropping patterns and under PGPR application, a two-years field experiment (2015 and 2016) was arranged as factorial design based on randomized complete blocks (RCBD) with three replications. The first factor consisted of six cropping patterns including sole cropping of fennel, sole cropping of common bean, and different intercropping ratios of fennel to common bean (1:1, 2:2, 3:2, 4:2), whereas the second factor included the application and non-application of PGPR. The results showed that the highest seed yields of common bean (2474.83 kg ha−1) and fennel (2730.08 kg ha−1) were produced with sole cropping combined under PGPR application. The fennel essential oil (EO) and seed oil (fixed oil) content in all intercropping patterns were higher than those in sole cropping. Furthermore, under PGPR application, the seed yield, EO content, EO yield, fixed oil content and oil yield of fennel increased by 20.9, 16.4, 39.3, 10.3 and 33.3 %, respectively, compared with control. Based on the chemical analysis of fennel EO, the main constituents were (E)-anethole (73.71–81.10%), fenchone (3.44–6.18%), limonene (3.49–5.82%) and methyl chavicol (4.06–7.22%). The major fatty acids in fennel fixed oil were oleic (77.17–82.90%), linoleic (6.50–8.97%) and palmitic acids (3.25–6.80%). The highest content of unsaturated fatty acids (oleic and linoleic acids) and (E)- anethole were obtained with intercropping ratios (fennel to common bean) of 2:2 and 3:2 under PGPR application, respectively. Furthermore, the highest land equivalent ratio (1.32) was obtained with intercropping ratio of 3:2 under PGPR application. Our findings showed that the intercropping ratio of 2:2 and 3:2 upon PGPR biofertilization may be suggested to farmers instead of sole cropping for enhancing the fennel EO and fixed oil quali-quantitative composition.