On a daily basis, a wide range of materials including inorganic nanoparticles (NPs) inadvertently find their way into the environment. Meanwhile, intentionally used NPs, such as the new generation of nanofertilizers (NFs) are designed to enhance agronomic production. However, their physicochemical properties and not-so-well understood effects raise potential risks to the plant reproductive cycle, specifically pollen development, a subject largely absent in academic research. Even slight contamination, deformation, or aberration of pollen could have enormous impacts on the ecosystem. Thus, our objective was to evaluate the influence of various metal-based NPs on sunflower pollen morphology and its yield. Nano-formulations were applied during the 2019–2021 agronomic seasons on two sunflower hybrids, Neostar and Edison, in Dolná Malanta, near Nitra, Slovak Republic. Pollen morphology findings indicated that conventional ZnSO4 had the most positive impact on the size of pollen grains compared to ZnO-NPs, Fe3O4-NPs, and the NP-free control. Gold-NPs on SiO2 mesoporous silica (AuSi-NPs) showed a statistically insignificant impact, while the use of TiO2-NPs in agriculture remained a topic of debate. Surprisingly, pollen characteristics did not fully correspond to crop yields. Despite causing a reduction in pollen grain size, the TiO2-NPs consistently showed the highest yield compared to other variants. Employing low concentrations of NFs did not notably alter pollen morphology, reinforcing our commitment to eco-friendly, precise, and sustainable agriculture.