In order to fully understand nanoscale heat transport it is necessary to spectrally characterize phonon transmission in nanostructures. Toward this goal we have developed a microfabricated phonon spectrometer. We utilize microfabricated superconducting tunnel junction (STJ)-based phonon transducers for the emission and detection of tunable, non-thermal and spectrally resolved acoustic phonons, with frequencies ranging from ∼100 to ∼870 GHz, in silicon microstructures. We show that phonon spectroscopy with STJs offers a spectral resolution of ∼15-20 GHz, which is ∼20 times better than thermal conductance measurements, for probing nanoscale phonon transport. The STJs are Al-Al x O y -Al tunnel junctions and phonon emission and detection occurs via quasiparticle excitation and decay transitions that occur in the superconducting films. We elaborate on the design geometry and constraints of the spectrometer, the fabrication techniques and the low-noise instrumentation that are essential for successful application of this technique for nanoscale phonon studies. We discuss the spectral distribution of phonons emitted by an STJ emitter and the 3 Current address: