We explore phonon-mediated quantum transport through electronic noise characterization of a commercial CMOS transistor. The device behaves as a single electron transistor thanks to a single impurity atom in the channel. A low noise cryogenic CMOS transimpedance amplifier is exploited to perform low-frequency noise characterization down to the single electron, single donor and single phonon regime simultaneously, not otherwise visible through standard stability diagrams. Single electron tunneling as well as phonon-mediated features emerges in rms-noise measurements. Phonons are emitted at high frequency by generation-recombination phenomena by the impurity atom. The phonon decay is correlated to a Lorentzian $1/f^2$ noise at low frequency.