Background: Studies have shown that the consumption of apples has a beneficial effect on cardiovascular diseases and some cancers, largely due to their micronutrient and phytoconstituent contents. Apple peel contains more polyphenols than the flesh but is also likely to contain pesticide residues. This study aimed to compare the contents of certain micronutrients and residual pesticide levels in peeled and unpeeled apples. Results: Peeled apples contained fewer pesticide residues at lower concentrations than unpeeled apples. However, whether samples were peeled or not, the exposure values for pesticide residues in apples never exceeded the acceptable daily intake (ADI), but ranged between 0.04 and 2.10% of the ADI in adults for food intake estimated at the 95th percentile (277 g per person per day). Determination of polyphenol, fibre, magnesium, and vitamin C levels showed that the nutritional differences observed between peeled and unpeeled apples were marginal. Conclusion: The consumption of apples, such as the apples tested in the present study, results in an exposure to pesticides that is low for unpeeled apples, and lower for peeled apples. Moreover, there was no significant loss of nutritional value from eating peeled apples based on the nutrients investigated.