Natural diamonds with a rich variety of optically blind and optically active nitrogen impurity centers were explored at a nano/microscale on the surface and in bulk by a number of advanced chemical and structural analytical tools in order to achieve a comprehensive characterization by establishing enlightening links between their analysis results. First, novel compositional relationships were established between high-energy X-ray photoelectron spectroscopy (XPS) and low-energy Fourier-transform infrared vibrational spectroscopy (FT-IR) signals of nitrogen impurity defects acquired in the microscopy mode at the same positions of the diamond surface, indicating the verification XPS modality for qualitative and quantitative FT-IR analysis of high concentrations of nitrogen and other chemical impurity defects in diamond. Second, depth-dependent spatial distributions of diverse photoluminescence (PL)-active nitrogen defects were acquired in the confocal scanning mode in an octahedral diamond and then for the first time corrected to the related Raman signals of the carbon lattice to rule out artefacts of the confocal parameter and to reveal different micron-scale ontogenetic layers in the impurity distributions on its surface. Third, intriguing connections between local structural micro-scale defects (dislocation slip bands of plastic deformation zones) visualized by optical microscopy and Raman microspectroscopy, and related distributions of stress-sensitive PL-active nitrogen impurity defects in the proximity of these planes inside bulk diamonds were revealed. These findings demonstrate the broad instrumental opportunities for comprehensive in situ studies of the chemical, structural, and mechanical micro-features in diamonds, from the surface into bulk.