Quantum spin-liquids are strongly correlated phases of matter displaying a highly entangled ground state. Due to their unconventional nature, finding experimental signatures of these states has proven to be a remarkable challenge. Here we show that the effects of local impurities can provide strong signatures of a Dirac quantum spin-liquid state. Focusing on a gapless Dirac quantum spin-liquid state as realized in NaYbO$_2$, we show that single magnetic impurity coupled to the quantum spin-liquid state creates a resonant spinon peak at zero frequency, coexisting the original Dirac spinons. We explore the spatial dependence of this zero-bias resonance, and show how different zero modes stemming from several impurities interfere. We finally address how such spinon zero-mode resonances can be experimentally probed with inelastic spectroscopy and electrically-driven paramagnetic resonance with scanning tunnel microscopy. Our results put forward impurity engineering as a means of identifying Dirac quantum spin-liquids with scanning probe techniques, highlighting the dramatic impact of magnetic impurities in a macroscopically entangled many-body ground state.