We report a detailed study of the nature of the RuGa3 in-gap states by means of precision microscopic methods: nuclear quadrupole resonance (NQR), nuclear magnetic resonance (NMR), and pump-probe spectroscopy. We observe a pronounced splitting of 69Ga nuclear spin-lattice relaxation curves below ∼40 K and between 70 and 145 K, although the corresponding NQR lines remain narrow over the entire temperature range under study. The slow relaxing component behaves like a typical phonon-induced relaxation way, while the fast relaxing one demonstrates signatures of paramagnetic (below ∼40 K) and activation (between 70 and 145 K) mechanisms. Moreover, additional Ga’ and Ga’’ positions with anomalously low electric field gradient were revealed for the first time for IrIn3-type structure gallides, which stay almost unchanged, at least up to 77 K. The observed microscopic features are accompanied with in-gap states saturation or depleting, which is seen as the resistivity mechanism crossover at ∼180 K and electron localization below 145 K evidenced by pump-probe spectroscopy. Based on our experimental results, we associate this pseudo-gap like behavior with inhomogeneously distributed electronic density defects, which manifest at both micro- (nuclear spin and phonon dynamics) and macroscale (bulk transport properties such as resistivity).