Bell pepper (Capsicum annuum L.) is a commercially important and nutritionally rich vegetable crop in the Solanaceae family. Alkaline stress (AS) can disrupt growth, metabolism, and, particularly, nutritional quality. This study aims to evaluate the role of iron oxide nanoparticles (FeNP) in mitigating AS and enhancing plant growth and metabolic functions by conducting experiments under controlled greenhouse conditions with four main treatments: AS (irrigating plants with alkaline salts mixture solution); FeNP (foliar application of FeO nanoparticles at 100 mg L¹); AS + FeNP (integrated treatment of AS and FeNP); and CK (control). The results clearly demonstrated that the AS treatment negatively affects plant biomass, photosynthetic attributes, membrane integrity, carbohydrate metabolism, and the balance of the antioxidant system. Additionally, key phenolic and flavonoid compounds decreased under the AS, indicating a detrimental effect on the plant's secondary metabolites. In contrast, the application of FeNP under the AS not only improved growth and photosynthetic attributes but also enhanced membrane integrity and restored antioxidant balance. This restoration was driven by the accumulation of sugars (glucose, fructose, sucrose) and starch, along with key carbohydrate metabolism enzymes-sucrose phosphate synthase (SPS), sucrose synthase (SuSy), neutral invertase (NI), and vacuolar invertase (VI)-and their associated gene expression. The correlation analysis further revealed a tight regulation of carbohydrate metabolism at both enzymatic and transcript levels in all tissue types, except for SPS in the roots. Furthermore, the AS + FeNP treatment resulted in increased levels of key phenolics (dihydrocapsaicin, capsaicin, p-coumaric acid, sinapic acid, p-OH benzoic acid, p-OH benzaldehyde, and ferulic acid) and flavonoid compounds (dihydroquercetin, naringenin, kaempferol, dihydrokaempferol, and quercetin) compared to the AS treatment, thus suggesting that these secondary metabolites likely contribute to the stabilization of cellular structures and membranes, ultimately supporting improved physiological functions and resilience under stress. In conclusion, the application of FeNP demonstrate potential in enhancing the resilience of bell pepper plants against the AS by improving growth, carbohydrate metabolism, and the levels of secondary metabolites.