(1) Background: Overweight and obesity are emerging global problems causing multiple health complications. Excessive fat tissue content leads to chronic inflammation, which is why antioxidative compounds that could potentially reduce these processes are possible agents that could be supplemented in order to prevent metabolic complications of overweight and obesity. Apples and dwarf kiwis are good sources of antioxidative agents such as quercetin and chlorogenic acid. The aim of this study was to assess if apple and dwarf kiwi nutraceutical supplementation can improve the metabolic parameters of overweight adults. (2) Methods: 43 participants were enrolled in the double-blinded pilot study: 21 in the supplementation group and 22 in the placebo group. The one 1000 mg nutraceutical capsule contained 10% Chopin apple peel extract, 10% whole dwarf kiwi fruit extract, 75% Chopin apple core extract, and 5% rapeseed peptides. The supplementation group received two capsules/day for 60 days. (3) Results: The supplementation of the apple and kiwi product resulted in a lowering of ALT in the supplementation group (from 29.65 ± 19.02 UI/L to 23.80 ± 13.76 UI/L; p = 0.01). Subgroup analysis in men and women showed a significant decrease in total cholesterol level (from 220.15 ± 36.69 mg/dL to 208.43 ± 37.09 mg/dL; p = 0.04), non-HDL cholesterol (from 161.17 ± 41.00 mg/dL to 145.69 ± 41.75 mg/dL; p = 0.02) and ALT (from 25.41 ± 12.05 UI/L to 19.07 ± 6.13 UI/L; p = 0.01) in women and triglycerides levels (from 212.74 ± 127.15 mg/dL to 155.63 ± 80.61 mg/dL; p = 0.047) in men. (4) Conclusions: The supplementation of nutraceuticals from apples and dwarf kiwi led to improvements in lipid profile. It can be a possible new agent for counteracting overweight metabolic complications, however, larger group studies and more detailed tests are needed to support these preliminary findings. Keywords: dwarf kiwi; apples; overweight; obesity; metabolic syndrome; nutraceutical