Food matrix interactions with polyphenols can affect their bioavailability and as a consequence may modulate their biological effects. The aim of this study was to determine if the matrix and its processing would modulate the bioavailability and the postprandial nutrigenomic response to a dietary inflammatory stress of apple flavan-3-ol monomers. We carried out an acute randomized controlled study in minipigs challenged with a high fat meal (HFM) supplemented with raw fruit, puree, or apple phenolic extract with matched content of flavan-3-ol monomers. Fasting and postprandial blood samples were collected over 3 h to quantify flavan-3-ol monomers in sera by UPLC-Q-TOF/MS and to isolate peripheral blood mononuclear cells (PBMCs) for assessing the changes in the gene expression profile using a microarray analysis. When compared to the extract-supplemented meal, the peak of the total flavan-3-ol concentration was reduced by half with both raw apple and puree supplements. The apple matrices also affected the gene expression profile as revealed by the Principal Component Analysis of the microarray data from PBMCs which discriminated the supplementation of HFM with the polyphenol extract from those with raw apples or puree. A total of 309 genes were identified as differentially expressed by the apple-derived products compared to HFM, with 63% modulated only in the presence of the food matrix (apple and puree). The number of differentially modulated genes was higher with the puree (246) than with the unprocessed apple (182). Pathway enrichment analyses revealed that genes affected by the apple-derived products control inflammation and leukocyte transendothelial migration both involved in the onset of atherosclerotic processes. Overall, this study showed that the two apple matrices reduce the postprandial serum concentration of flavon-3-ols whereas they increase the nutrigenomic response of PBMCs. The biological processes identified as modulated by the apple products suggest an attenuation of the transient pro-inflammatory response induced by a HFM. The differences observed between the nutrigenomic responses support that the apple matrix and its processing affect the nutrigenomic response, probably by increasing the bioavailability of other apple phytochemicals. To conclude, this study raises awareness for considering the impact of the food matrix and its processing on the biological response of polyphenols in nutritional studies.