Abstract Background Research on intestinal microbiota has grown considerably, as well as the interest on probiotics’ supplementation effects on metabolism. Considering high prevalence rates of metabolic diseases linked by insulin resistance, we performed a systematic review of existing literature which addressed the role of probiotics in modulating insulin sensitivity in animals and humans. Methods This systematic review was based on PRISMA guidelines. Searches for original articles published in English from 1990 to January 2020 were made in the electronic database of PubMed from the National Library of Medicine, using Medical Subject Headings to identify longitudinal studies conducted in animals and humans which reported effects of probiotics in a variety of insulin resistance parameters. Results Overall, results from 27 probiotic interventions (Lactobacillus, Bifidobacterium, Clostridium and Akkermansia) indicated significant beneficial changes in insulin resistance measures in animal studies. Additionally, they improved lipid profile, inflammatory and oxidative markers, short-chain fatty acids production and microbiota composition. In seven clinical trials, samples and designs were heterogeneous. Five showed benefits in insulin resistance parameters and in two others no effect was detected. Conclusion Available data regarding the effects of certain probiotics do not guarantee sustained amelioration of insulin resistance in humans. Consistent beneficial results for intestinal barrier function, immune system and metabolism were reported in animals may encourage long-term randomized clinical trials in people with obesity and cardiometabolic risk. Whether supplementation with probiotics in combination with medications and/or prebiotics, associated with a healthy lifestyle, will prove useful to attenuate insulin resistance requires further investigation.