This study aimed to synthesize, characterize, and evaluate the effect of cocamidopropyl betaine-stabilized MnO2 nanoparticles (NPs) on the germination and development of pea seedlings. The synthesized NPs manifested as aggregates ranging from 50–600 nm, comprising spherical particles sized between 19 to 50 nm. These particles exhibited partial crystallization, indicated by peaks at 2θ = 25.37, 37.62, 41.18, 49.41, 61.45, and 65.79°, characteristic of MnO2 with a tetragonal crystal lattice with a I4/m spatial group. Quantum chemical modelling showed that the stabilization process of MnO2 NPs with cocamidopropyl betaine is energetically advantageous (∆E > 1299.000 kcal/mol) and chemically stable, as confirmed by the positive chemical hardness values (0.023 ≤ η ≤ 0.053 eV). It was revealed that the interaction between the MnO2 molecule and cocamidopropyl betaine, facilitated by a secondary amino group (NH), is the most probable scenario. This ascertain is supported by the values of the difference in total energy (∆E = 1299.519 kcal/mol) and chemical hardness (η = 0.053 eV). These findings were further confirmed using FTIR spectroscopy. The effect of MnO2 NPs at various concentrations on the germination of pea seeds was found to be nonlinear and ambiguous. The investigation revealed that MnO2 NPs at a concentration of 0.1 mg/L resulted in the highest germination energy (91.25%), germinability (95.60%), and lengths of roots and seedlings among all experimental samples. However, an increase in the concentration of preparation led to a slight growth suppression (1–10 mg/L) and the pronounced inhibition of seedling and root development (100 mg/L). The analysis of antioxidant indicators and phytochemicals in pea seedlings indicated that only 100 mg/L MnO2 NPs have a negative effect on the content of soluble sugars, chlorophyll a/b, carotenoids, and phenols. Conversely, lower concentrations showed a stimulating effect on photosynthesis indicators. Nevertheless, MnO2 NPs at all concentrations generally decreased the antioxidant potential of pea seedlings, except for the ABTS parameter. Pea seedlings showed a notable capacity to absorb Mn, reaching levels of 586.5 μg/L at 10 mg/L and 892.6 μg/L at 100 mg/L MnO2 NPs, surpassing the toxic level for peas according to scientific literature. However, the most important result was the observed growth-stimulating activity at 0.1 mg/L MnO2 NPs stabilized with cocamidopropyl betaine, suggesting a promising avenue for further research.