Constraining planetary heat flux is crucial to understanding thermal evolution. NASA’s Juno mission has taken advantage of its evolving orbit to perform close flybys of Ganymede, Europa and Io in 2021–2024. These encounters enabled observations of the microwave emission of the Jovian moons using Juno’s Microwave Radiometer (MWR), which detects thermal emission from depths ranging from centimeters to kilometers. Juno MWR observations of Ganymede show increasing brightness temperature at lower frequencies, indicating thermal emission from deeper layers, with temperatures correlated with terrain and anticorrelated with visible albedo. Modeling based on these data constrains Ganymede’s ice shell thickness and internal structure. At Europa, MWR data suggest a 29 ± 10 km thick ice shell. Decreasing brightness temperatures at lower frequencies imply a fractured, porous shell. Io flybys in 2023–2024 reveal low-frequency brightness temperature gradient, suggesting deep thermal anomalies, while higher-frequency data correlate with known volcanic centers observed in the infrared.