In recent decades, the laws of thermodynamics have been pushed down to smaller and smaller scales, within the field of stochastic thermodynamics and state-of-art experiments performed on mesoscopic systems. But these measurements concern mostly thermal properties of electrons and photons. Here we report on the measurements of thermal fluctuations of a single mechanical mode in-equilibrium with a heat reservoir. The device under study is a nanomechanical beam with a first flexure resonating at 3.8MHz, cooled down to temperatures in the range from 100mK to 400mK. The technique is constructed around a microwave opto-mechanical setup using a cryogenic High Electron Mobility Transistor, and is based on two parametric amplifications implemented in series: an in-built opto-mechanical 'blue-detuned' pumping plus a Traveling Wave Parametric Amplifier stage. We demonstrate our ability to resolve energy fluctuations of the mechanical mode in real-time up to the fastest relevant speed given by the mechanical relaxation rate. The energy probability distribution is then exponential, matching the expected Boltzmann distribution. The variance of fluctuations is found to be $(k_B T)^2$ with no free parameters. Our microwave detection floor is about 3 Standard Quantum Limit at 6GHz; the resolution of our fastest acquisition tracks reached about 100 phonons, and is related to the rather poor opto-mechanical coupling of the device ($g_0/2\pi\approx 0.5~$Hz). This result is deeply in the classical regime, but shall be extended to the quantum case in the future with systems presenting a much larger $g_0$ (up to $2\pi\times 250~$Hz), potentially reaching the resolution of a single mechanical quantum. We believe that it will open a new experimental field: phonon-based quantum stochastic thermodynamics, with fundamental implications for quantum heat transport and macroscopic mechanical quantum coherence.