The past two decades have been characterised by extraordinary accomplishments in the control of matter and light. This has opened up new avenues for atomic, molecular and optical physics including novel tests of physics beyond the Standard Model. The combined use of effective field theories, precision computations and highly accurate experimental data makes spectroscopy a competent and reliable testing ground for dark sectors in the keV-MeV range. We present the EFT framework to carry out such study and propose two main phenomenological applications: purely leptonic systems such as muonium and semileptonic systems, where the newly attained proton radius has pushed the theoretical precision of hydrogen and muonic hydrogen spectroscopy.