Harvesting of silage maize in late autumn on waterlogged soils may result in several ecological problems such as soil compaction and may subsequently be a major threat to soil fertility in Europe. It was hypothesized that perennial energy crops might reduce the vulnerability for soil compaction through earlier harvest dates and improved soil stability. However, the performance of such crops to be grown on soil that are periodically waterlogged and implications for soil chemical and microbial properties are currently an open issue. Within the framework of a two-year pot experiment we investigated the potential of the cup plant (Silphium perfoliatum L.), Jerusalem artichoke (Helianthus tuberosus), giant knotweed (Fallopia japonicum × bohemica), tall wheatgrass (Agropyron elongatum), and reed canary grass (Phalaris arundinacea) for cultivation under periodically waterlogged soil conditions during the winter half year and implications for soil chemical and biological properties. Examined perennial energy crops coped with periodical waterlogging and showed yields 50% to 150% higher than in the control which was never faced with waterlogging. Root formation was similar in waterlogged and non-waterlogged soil layers. Soil chemical and microbial properties clearly responded to different soil moisture treatments. For example, dehydrogenase activity was two to four times higher in the periodically waterlogged treatment compared to the control. Despite waterlogging, aerobic microbial activity was significantly elevated indicating morphological and metabolic adaptation of the perennial crops to withstand waterlogged conditions. Thus, our results reveal first evidence of a site-adapted biomass production on periodical waterlogged soils through the cultivation of perennial energy crops and for intense plant microbe interactions.