Apple is one of the most commonly consumed fruits worldwide and it has been associated with several health effects, especially on plasma cholesterol and risk of cardiovascular disease both in human and animal studies. By using an untargeted metabolomics approach we wanted to investigate whether supplementation of whole apple or processed apple products affect the human plasma metabolome. Therefore, 24 healthy volunteers were recruited for a comprehensive 5 × 4 weeks dietary crossover study and receiving supplement of whole apples (550 g/day), clear and cloudy apple juices (500 ml/day), dried apple pomace (22 g/day), or no supplement. Plasma was collected for analysis after an overnight fast and analysed by UPLC-ESI-TOF-MS. Discriminative features revealed by Partial Least Square-Discriminant Analysis showed whole apple and apple pomace having generally a stronger modifying effect of the plasma metabolome than the other apple products. We observed an effect on branched-chain amino acids and aromatic amino acids degradation, and a decreased use of lipid fuels indicating an improvement in glucose utilisation. A reduced level of plasma bile acids after apple consumption may indicate less re-absorption from the gut. Some lysoPCs and a steroid hormone precursor decreased as well, indicating a reduced outbound cholesterol transport from the liver and less use of cholesterol for steroid synthesis. In the light of these results, we speculate that apple and/or apple pomace seems to affect cholesterol homeostasis by several mechanisms.