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Abstract Phonon polaritons – quasiparticles formed by strong coupling of infrared (IR) light with lattice vibrations in polar materials – can be utilized for surface-enhanced infrared absorption (SEIRA) spectroscopy and even for vibrational strong coupling with nanoscale amounts of molecules. Here, we introduce and demonstrate a compact on-chip phononic SEIRA spectroscopy platform, which is based on an h-BN/graphene/h-BN heterostructure on top of a metal split-gate creating a p-n junction in graphene. The metal split-gate concentrates the incident light and launches hyperbolic phonon polaritons (HPhPs) in the heterostructure, which serves simultaneously as SEIRA substrate and room-temperature infrared detector. When thin organic layers are deposited directly on top of the heterostructure, we observe a photocurrent encoding the layer’s molecular vibrational fingerprint, which is strongly enhanced compared to that observed in standard far-field absorption spectroscopy. A detailed theoretical analysis supports our results, further predicting an additional sensitivity enhancement as the molecular layers approach deep subwavelength scales. Future on-chip integration of infrared light sources such as quantum cascade lasers or even electrical generation of the HPhPs could lead to fully on-chip phononic SEIRA sensors for molecular and gas sensing.