Modulation of the gut microbiota may help in treating obesity by improving host metabolic health. We aimed to evaluate the effects of probiotics or symbiotics on body weight and serum metabolite profile in women with obesity. A double-blind, parallel, randomized, controlled clinical trial was conducted with 32 adult women with body mass index ranging from 30 to 34.9 kg m-2. Volunteers followed a low-energy diet and were subjected to 8 weeks intervention: probiotic group (PG - Bifidobacterium lactis UBBLa-70, n = 10), symbiotic group (SG - Bifidobacterium lactis UBBLa-70 and fructooligosaccharide, n = 11), or control group (CG - placebo, n = 11). Analyses of anthropometric variables, gut microbiota and serum metabolites by 1H nuclear magnetic resonance (NMR) were performed at baseline and after the intervention. Multivariate statistics showed that all groups presented a decrease in glycerol and increase in arginine, glutamine and 2-oxoisovalerate. Therefore, a low-energy diet per se promoted changes in the metabolite profile related to decreased inflammation and positive effects on body weight. SG presented unique changes in metabolites (increase in pyruvate and alanine and decrease in citrate and BCAA). Negative correlations between arginine and glutamine with fat mass were observed in the SG. PG presented a decrease in 1H NMR lipid signals and negative correlation between Verrucomicrobia and Firmicutes with (CH2)n lipids. Both probiotics and symbiotics promoted changes in metabolites related to improved metabolic health. Specific metabolite changes following symbiotic intervention might suggest some advantage in providing Bifidobacterium lactis in combination with fructooligosaccharide in a low-energy diet, rather than probiotics or diet alone. Clinical trial: NCT02505854.