Radiant heating is a well-established solution that is widely adopted in existing and new nearly zero energy buildings (NZEBs). Underfloor heating (UFH) is known for its many advantages, e.g., allowing access to low-grade heat sources such as heat pumps and low temperature district heating (LTDH) systems, and secure comfortable indoor environment. This study presents a long-term monitoring campaign of an NZEB building fully covered with a UFH system. Monitoring covers approximately one entire heating season, with the experiment aiming to decrease the operational indoor temperature and energy use for space heating while investigating the occupants’ acceptance to this new thermal comfort situation and registering their feedback about perceived thermal comfort. The experiment results show that there is a significant reduction in the operation of the hydraulic system and water circulation in the UFH that is negatively perceived by the occupants who are used to feeling the warm floor. The paper highlights that the UFH, in combination with occupant’s comfort preferences, can be the reason for NZEBs to operate with elevated indoor temperatures and to use more energy than anticipated. Results indicate that UFH in bathrooms is operated all year long due to occupants striving to feel the warm floor. The findings can significantly contribute to the advancement of innovative control strategies for achieving thermal comfort in NZEB buildings with radiant water-based heating systems and consideration for other placement of radiant emitters in the spaces.