The postnatal period is critical for early development. Due to the great plasticity of the digestive tract, this period constitutes a unique window to orient the digestive phenotypes. Xylo-oligosaccharides (XOS) produced from the hydrolysis of non-starch polysaccharides (NSPs) by xylanase (Xyl.) are prebiotics acting on the caecal microbiota. In this work, we compared the effects on metabolome and caecal microbiota composition of early (starter) or late (grower) supplementation with a mixture of xylanase and XOS (Xyl.XOS) with an Eimeria tenella challenge. Chicks fed a basal diet rich in NSPs (wheat/rye) were divided into four groups: without additive (D0-D22), with a supplementation of Xyl.XOS during the start-up period (D0-D9), the growth period (D10-D22), or during the entire period (D0-D22). Based on this full factorial design, effects on performance as well as on the metabolome (RMN) and caecal microbiome (16S rRNA sequencing) were assessed at D9 and D22. During the start-up period, the addition of Xyl.XOS has a positive effect on growth. At D9, a decrease in Short Chain Fatty Acids (SCFAs) and Lachnospiraceae, producers of SCFAs observed in the caeca of supplemented animals with Xyl.XOS. In contrast, supplementation in the starter diet alone increased SCFA production until D22. We are actually evaluating the effect of this early supplementation on the microbiota at D22. In animals inoculated with E. tenella, the supplementation with Xyl.XOS in grower reduced significantly the deleterious effects of infection on growth while early supplementation had no detectable effect. In conclusion, early supplementation with Xyl.XOS has a short and medium term effect on the metabolites and growth of the animals.