The suitability of miscanthus biomass for anaerobic digestion has already been confirmed by several studies. However, it is rarely used as feedstock in biogas plants, mainly due to uncertainty about the optimal harvest regime with regard to the long‐term methane hectare yield and resilience of the crop to green cutting. The recommended green‐cut date for the only commercially available genotype Miscanthus × giganteus (M×g) ranges from September to November. This timeframe is too broad for agricultural practice and needs to be both narrowed down and further specified for different genotypes. The aim of this study was to identify the most suitable harvest window for an autumn green cut of miscanthus, which delivers both a high dry matter and methane yield while securing the long‐term productivity of the crop. A further objective was to quantify the effect of genotypic differences, such as leaf to stem ratio, on the substrate‐specific biogas and methane yield. For these purposes, a field trial with four genotypes (M×g, GNT1, GNT3, Sin55) was conducted over 2 years (2016/2017) and harvested at 2‐week intervals on three dates between mid‐September to mid‐October. Methane hectare yield ranged from 3,183 m³ CH4 ha−1 a−1 (Sin55) to 5,265 m³ CH4 ha−1 a−1 (M×g), which is mainly influenced by dry matter yield. The substrate‐specific methane yield was higher for the leaf (311.0 ml CH4 (g oDM)‐1) than the stem fraction (285.1 ml CH4 (g oDM)‐1) in all genotypes due to lower lignin content of leaves. Of all genotypes, M×g showed the highest and Sin55 the lowest nutrient use efficiency. We conclude that miscanthus in Germany should be harvested in October to maximize methane yields and nutrient recycling and minimize yield reduction. Additionally, to increase methane hectare yields even further, future miscanthus breeding should focus on a higher leaf proportion.