Growth monitoring during the early stages of vapor deposition is of prime importance to understand the growth process, the microstructure, and thus the overall layer properties. We demonstrate that phonons can be used as an extremely sensitive probe to monitor the real-time evolution of film microstructure during growth, from incipient clustering to continuous film formation. For that purpose, a silicon nitride membrane-based sensor is fabricated to measure the in-plane thermal conductivity of thin film (conductive or nonconductive) samples. Operating with the 3 omega-Volklein method at low frequencies, the sensor shows an exceptional resolution down to Delta(kappa.t) = 0.065 W/mKnm, enabling accurate measurements even in poor conductive samples. Validation of the sensor performance is done by growth characterization of organic and metallic thin films to tackle the low to high thermal-conductivity range. In both cases, at early stages of growth, the extreme sensitivity of the technique has revealed an initial reduction of the effective thermal conductance of the supporting amorphous membrane, K, related to the surface phonon scattering enhanced by the incipient nanoclusters formation. As cluster coalescence advances, K reaches a minimum to rise up upon the percolation threshold. Subsequent island percolation produces a sharp increase of the conductance and once the surface coverage is completed K increases linearly with thickness. The thermal conductivity of the deposited films is also obtained from the slope of K with thickness.