Orthogonal techniques were used to track manganese nanoparticles (MnNPs) in Capsicum annuum L. leaf tissue and cell compartments and subsequently to explain the mechanism of uptake, translocation, and cellular interaction. C. annuum L was cultivated and foliarly exposed to MnNPs (100 mg/ L, 50 mL/per leaf) before analysis by using scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS) as well as dark-field hyperspectral and two-photon microscopy. We visualized the internalization of MnNP aggregates from the leaf surface and observed particle accumulation in the leaf cuticle and epidermis as well as spongy mesophyll and guard cells. These techniques enabled a description of how MnNPs cross different plant tissues as well as selectively accumulate and translocate in specific cells. We also imaged abundant fluorescent vesicles and vacuoles containing MnNPs, indicating likely induction of autophagy processes in C. annuum L., which is the bio-response upon storing or transforming the particles. These findings highlight the importance of utilizing orthogonal techniques to characterize nanoscale material fate and distribution with complex biological matrices and demonstrate that such an approach offers a significant mechanistic understanding that can inform both risk assessment and efforts aimed at applying nanotechnology to agriculture.