In the search for sustainable agricultural methods for industrial crops, peppermint (Menthapiperita) was strip intercropped with soybean (Glycine max). Intercropping peppermint with soybean resulted in yield and quality increases in the essential oil, compared to sole peppermint cultivation. The yield was higher by about 50% on an equal land area basis and higher percentages of menthol and lower percentages of menthofuran and menthyl acetate improved the quality of the oil. Intercropped peppermint leaf number per node, leaf area, perimeter and leaf area index (LAI) were greater along with the internode length and thickness, when compared to monocultured plants. Total leaf peltate trichome number was higher in intercropped peppermint plants and was positively correlated with greater essential oil productivity. Leaf and stem dry weight were higher in intercropped peppermint. Total chlorophyll and carotenoid content also increased in intercropped peppermint plants, whereas no variation was found for total soluble protein. In peppermint, no significant differences were found in the CO2 compensation point between the two cropping systems, whereas intercropped plants showed a higher stomatal conductance at low CO2 concentration. The relationship between primary and secondary peppermint plant metabolism was also discussed.