The objective was to investigate the effects of increasing levels of the soy galactooligosaccharides (GOS) raffinose and stachyose in feed on performance and gastrointestinal health including AMEn, nitrogen retention and ceca microbiome in young chickens in a randomized complete block design. Results of performance, intestinal morphology and permeability and cell immunology have been published previously. A 21-d trial was conducted with 400 d-old Cobb 500 male chickens placed in 50 battery cages (8 birds/cage; 0.04 m2/bird). Replicate cages were assigned to one of five treatments: a control diet devoid of the soy GOS based on soy protein isolate (SPI) or the same SPI diet with 0.9, 1.8, 2.7 or 3.6% added GOS (a mix of stachyose and raffinose, 4:1 ratio, as found in soybean meal). Birds had ad libitum access to feed and water. Feed intake and excreta output were measured from d12-14 and d18-21 and homogenous excreta samples were collected to determine nitrogen retention and AMEn. At d21, ceca digesta was collected for microbiome analysis. The V4 region of the bacterial 16S rRNA gene was sequenced on a MiSeq sequencer. Data were analyzed by one-way ANOVA. Means were compared by Tukey’s multiple comparison test. Linear and quadratic regressions were used to investigate the dose-response of GOS in diets. The microbiome data were analyzed by using the QIIME2 software package. Linear discriminant analysis effect size was performed to identify the microbiome signature for differentiating groups. At d14, both linear (p<0.01) and quadratic effects (p<0.01) were observed for nitrogen retention, the maximum value being 70.20% at 1.24% GOS, based on the quadratic regression. At d21, nitrogen retention decreased linearly (p<0.001) with increasing GOS level. AMEn increased according to a quadratic regression at d14 (p<0.03) and d21 (p<0.001), the maximum values being 4,073 kcal/kg DM at 1.61% GOS and 3,911 kcal/kg DM at 1.44% GOS, respectively. GOS supplementation significantly affected ceca microbiome. 1.8, 2.7 and 3.6% GOS significantly decreased alpha diversity including Shannon Index and the number of Observed Amplicon Sequence Variants (ASVs) compared to 0 and 0.9% GOS, and showed distinct cluster based on Bray-Curtis and Jaccard distances. Ruminococcus (ASV14, ASV27 and ASV28), Coprococcus (ASV22) and Oscillospira (ASV59) were increased with increasing GOS-levels, while Lachnospiraceae (ASV40), Butyricicoccus pullicaecorum (ASV127) were increased in the control group. Blautia (ASV80) had higher abundance in the control and 0.9% GOS groups.