The calculation of the natural lineshape of an excited two-level system (TLS) has long been known to be gauge dependent, with experiments and classical predictions in better agreement with the lineshape calculated with the dipole gauge ($-\mathbf{r}·\mathbf{E}$ coupling). We show that by using a Coulomb-gauge ($\mathbf{p}·\mathbf{A}$ coupling) Hamiltonian truncated in a manner consistent with the gauge principle, the correct output spectrum can, in fact, be obtained. For TLSs undergoing dynamics arising from additional Hamiltonian couplings, we also show that the master equation is gauge invariant under the same conditions of validity as the Markov approximation, despite different gauges having different spectral densities. These results highlight the importance of using correctly truncated gauge-invariant Hamiltonians in input-output theory for accurate frequency-dependent spectra, even in weak-coupling regimes.

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