The reasons for the early Holocene temperature discrepancy between northern hemispheric model simulations and paleoclimate reconstructions—known as the Holocene temperature conundrum—remain unclear. Using hydrogenisotopes of fluid inclusion water extracted from stalagmites from the Milandre Cave in Switzerland, we established a mid-latitude European mean annual temperature reconstruction for the past 14,000 years. Our Milandre Cave fluid inclusion temperature record (MC-FIT) resembles Greenland and Mediterranean sea surface temperature trends but differs from recent reconstructions obtained from biogenic proxies and climate models. The water isotopes are further synchronized with tropical precipitation records, stressing the Northern Hemisphere signature. Our results support the existence of a European Holocene Thermal Maximum and data-model temperature discrepancies. Moreover, data-data comparison reveals a significant latitudinal temperature gradient within Europe. Last, the MC-FIT record suggests that seasonal biases in the proxies are not the primary cause of the Holocene temperature conundrum.