The production of heat by mitochondria is critical for maintaining body temperature, regulating metabolic rate, and preventing oxidative damage to mitochondria and cells. Until the present, mitochondrial heat production has been characterized only by methods based on fluorescent probes, which are sensitive to environmental variations (viscosity, pH, ionic strength, quenching, etc.). Here, for the first time, the heat release of isolated mitochondria was unambiguously measured by a diamond thermometer (DT), which is absolutely indifferent to external non-thermal parameters. We show that during total uncoupling of transmembrane potential by CCCP application, the temperature near the mitochondria rises by 4–22 ℃ above the ambient temperature with an absolute maximum of 45 ℃. Such a broad variation in the temperature response is associated with the heterogeneity of the mitochondria themselves as well as their aggregations in the isolated suspension. Spontaneous temperature bursts with comparable amplitude were also detected prior to CCCP application, which may reflect involvement of some mitochondria to ATP synthesis or membrane potential leaking to avoid hyperproduction of reactive oxygen species. The results obtained with the diamond temperature sensor shed light on the “hot mitochondria” paradox.