There is lack of information about the effects of nanoparticles (NPs) on cucumber fruit quality. This study aimed to determine possible impacts on carbohydrates, proteins, mineral nutrients, and antioxidants in the fruit of cucumber plants grown in soil treated with CeO2 and ZnO NPs at 400 and 800 mg/kg. Fourier transform infrared spectroscopy (FTIR) was used to detect changes in functional groups, while ICP-OES and μ-XRF were used to quantify and map the distribution of nutrient elements, respectively. Results showed that none of the ZnO NP concentrations affected sugars; however at 400 mg/kg, CeO2 and ZnO NPs increased starch content. Conversely, CeO2 NPs did not affect starch content but impacted nonreducing sugar content (sucrose). FTIR data showed changes in the fingerprint regions of 1106, 1083, 1153, and 1181, indicating that both NPs altered the carbohydrate pattern. ZnO NPs did not impact protein fractionation; however, CeO2 NPs at 400 mg/kg increased globulin and decreased glutelin. Both CeO2 and ZnO NPs had no impact on flavonoid content, although CeO2 NPs at 800 mg/kg significantly reduced phenolic content. ICP-OES results showed that none of the treatments reduced macronutrients in fruit. In case of micronutrients, all treatments reduced Mo concentration, and at 400 mg/kg, ZnO NPs reduced Cu accumulation. μ-XRF revealed that Cu, Mn, and Zn were mainly accumulated in cucumber seeds. To the best of the authors’ knowledge this is the first report on the nutritional quality of cucumber fruit attributed to the impact of CeO2 and ZnO NPs.