Emerging quantum technologies require mastering thermal management, especially at the nanoscale. It is now accepted that thermal metamaterial-based phonon manipulation is possible, especially at sub-kelvin temperatures. In these extreme limits of low temperatures and dimensions, heat conduction enters a quantum regime where phonon exchange obeys the Landauer formalism. Phonon transport is then governed by the transmission coefficients between the ballistic conductor and the thermal reservoirs. Here we report on ultra-sensitive thermal experiments made on ballistic 1D phonon conductors using a micro-platform suspended sensor. Our thermal conductance measurements attain a power sensitivity of 15 attoWatts Hz−−−√−1 around 100 mK. Ballistic thermal transport is dominated by non-ideal transmission coefficients and not by the quantized thermal conductance of the nanowire itself. This limitation of heat transport in the quantum regime may have a significant impact on modern thermal management and thermal circuit design.