The effects of increased intake of dietary fiber as either whole grain rye or as resistant starch compared to a typical low dietary fiber Western-style diet on the metabolomics responses was studied in gastrointestinal content and tissue, peripheral plasma and urine using a multicompartmental non-targeted liquid chromatography-mass spectrometry (LC-MS) approach in pigs. Both unsupervised and supervised multivariate analyses were used to study differences between the intervention groups, revealing significant effects of the dietary intervention on gastrointestinal contents and urine metabolites. Consumption of a diet composed of whole grain rye flakes and enzyme treated wheat bran increased gastrointestinal content of novel sulfate- and acetic acid conjugated oxylipins, and urinary secretion of phenolic compounds. Furthermore, potential gastrointestinal and urinary biomarkers for consumption of resistant starch, whole grain rye, and a low dietary fiber intake were detected using multi-block analysis. This study provides insight into microbial fermentation products in the gastrointestinal tract, and suggests a potential role in sulfate conjugation of metabolites on the bioavailability of ingested nutrients.