The spatial root distribution of plant species is generally altered by intra- and interspecific competition. The assessment of species specific root distribution in intercrops was limited so far because of the difficulties to identify roots on a species level. We investigated horizontal and vertical root distribution of eight winter faba bean genotypes (Vicia faba L.) and one winter wheat cultivar (Triticum aestivum L.) grown in sole stands and in 50/50 substitutive row intercrops.Root samples were taken within and between rows with a root auger down to 60 cm soil depth in May 2015 and May 2016 at a field site in central Germany. We used Fourier transform infrared (FTIR) spectroscopy for root species identification. Vertical root distribution was described by the equation y = 1 - βd according to Gale and Grigal (1987).Horizontal root distribution did not differ between bean and wheat and between sole stands and intercrops averaged across the eight bean genotypes: Bean and wheat root biomass was on average 65% lower between rows than within rows in sole stands and in intercrops. Both species proliferated into the soil space between the rows and into the intercropping partner’s row to a similar extent. Bean developed 36% of its root biomass in 0–10 cm soil depth, while wheat had 51%. Bean and wheat had shallower roots within their own row in intercrops (βbean = 0.933; βwheat = 0.858) compared to their own row in sole stands (βbean = 0.945; βwheat = 0.902). In the intercrops both species occupied deeper soil layers within their partner’s row (βbean = 0.947; βwheat = 0.960) compared to their own row (βbean = 0.933; βwheat = 0.858). This change in vertical root distribution was more pronounced for wheat than for bean. Bean genotypes grown in sole stands did not differ in their horizontal and vertical root distribution. However, there were significant differences between bean genotypes within wheat rows in the intercrops: bean genotype Vf6 had the largest horizontal spread but the most shallow root growth within the wheat row, while Vf5 showed the lowest horizontal spread and the highest root fractions in deep soil layers within the wheat row. The alteration of the vertical root distribution of both species in intercrops, compared to the sole crops, could lead to a better resource utilization and an intercrop advantage.