Weeds are the major biotic source of yield losses with an average of 19–51 % yield decrease. Beside this negative effect, they are a food source and habitat for insects and reduce the risk of soil erosion. Due to the heterogeneous soil conditions within a field, the distribution of weeds is uneven and therefore a uniform regulation is not always necessary. Additionally, mechanical weeding can lead to crop injuries and decreases soil quality. Site-specific weed management can reduce the drawbacks of weeding regulation. Precision application of herbicides is well known and practiced, however for mechanical weeding this is not the case. Site-specific mechanical weeding was tested in a maize (Zea mays L.) trial in the northwest of Germany in 2021 and 2022. In this research, multispectral images from unmanned aerial vehicles (UAV) were used to detect weeds with an overall accuracy between 85 and 92 %. These images were used to generate application maps. Two weed control thresholds, based on the weed cover (WC) and relative weed cover (RWC) with three threshold levels each were compared with uniform weeding. In 2021, higher maize yields (1879 g m−2 to 533 g m−2) and lower weed biomass (1151 g m−2 to 731 g m−2) were observed due to higher precipitation than in 2022. The different treatments did differ neither in maize yield nor in weed biomass. However, significantly less area was hoed in the site-specific treatments (−58 %), especially the treatments based on the RWC (−83 %). This study shows the potential of site-specific mechanical weed management and the RWC as weed control thresholds to promote biodiversity and reduce negative effect of weeding.