Carbon-based nanoparticles (CBNs) are nanomaterials that have been shown to be plant growth regulators. Here, we investigated the effects of long-term exposure to multi-walled carbon nanotubes (MWCNTs) on the growth of three important crops (barley, soybean, and corn). The tested species were cultivated in hydroponics supplemented with 50 μg/mL MWCNTs. After 20 weeks of continuous exposure to the nanomaterials, no significant toxic effects on plant development were observed. Several positive phenotypical changes were recorded, in addition to the enhancement of photosynthesis in MWCNT-exposed crops. Raman spectroscopy with point-by-point mapping proved that the MWCNTs in the hydroponic solution moved into all tested species and were distributed in analyzed organs (leaves, stems, roots, and seeds). Our results confirmed the significant potential of CBN in plant agriculture. However, the documented presence of MWCNTs in different organs of all exposed crops highlighted the importance of detailed risk assessment of nanocontaminated plants moving into the food chain.