Aquifer thermal energy storage (ATES) is a key concept for the use of renewable energy resources. Interest in ATES performed at high temperature (HT-ATES; > 60 °C) is increasing due to higher energetic efficiencies. HT-ATES induces temperature fluctuations that exceed the natural variability in shallow aquifers, which could lead to adverse effects in subsurface ecosystems by altering the groundwater chemistry, biodiversity, and microbial metabolic activity, resulting in changes of the groundwater quality, biogeochemical processes, and ecosystem functions. The aim of this study was to emulate the initial operating phase of a HT-ATES system with a short-term infiltration of warm water into Pleistocene sandur sediment and, consequently, to monitor the thermal effects on the groundwater microbiome inhabiting an imitated affected space of an HT-ATES system. Therefore, local groundwater was withdrawn, heated up to 75 °C, and re-infiltrated into a shallow aquifer located near Wittstock/Dosse (Brandenburg, Germany) for around five days. Groundwater samples taken regularly before and after the infiltration were analyzed by 16S rRNA gene amplicon sequencing for microbial diversity analyses as well as total cell counting. During the infiltration, a thermal plume with groundwater temperatures increasing from 9 ± 2 to up to ~65 °C was recorded. The highest temperature at which groundwater samples were taken was 34.9 °C, a temperature typically arising in the affected space of an HT-ATES system. The microbial communities in the groundwater were mainly composed of Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, and Actinobacteria, and the total cell numbers ranged from 3.2 * 104 to 3.1 * 106 cells ml-1. Neither the compositions of the microbial communities nor the total number of cells in groundwater were significantly changed upon moderate temperature increase, indicating that the diverse groundwater microbiome was resilient to the temporally limited heat stress.