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Intrabody Nanonetworks (IBN) are composed of nanosensors that have tremendous potential to enable cellular level monitoring and precision in drug delivery and diagnosis. Nanoscale communication using Electromagnetic (EM) waves propagation in the Terahertz (THz) band suffers from molecular absorption noise that has been regarded as the leading cause of heat generation along with antenna communication radiations. In the presented work, we propose a novel Temperature–Aware routing protocol (TA-IBN) that explicitly addresses the thermal related constraints of IBN. The proposed routing scheme aims at stabilizing the temperature in the whole network by avoiding congestion and preventing temperature rise in the heated regions. To avoid temperature rise, nanorouters estimate the temperature increase in their region and excludes data collection from the hotspots areas. Moreover, during data collection, nanonodes’ selection is also optimized based on data freshness to enable reporting of a more accurate state of physiological parameters with minimized antenna radiation exposure time. The temperature increase analysis provided in this work can also be used for safety health assessment in medical applications. We have evaluated the performance of TA-IBN by conducting extensive simulations using the Nano-SIM tool. In addition, we compare TA-IBN with the flooding scheme and Thermal-Aware Routing Algorithm (TARA) to gain further insights into our proposed protocol TA-IBN. The results obtained confirm that our protocol ensures safer intrabody routing and traffic distribution in different regions to normalize temperature rise, avoid congestion, and reduce the communication delay.