There are many benefits of both shakes and their ingredients, but there are a few key differences between Isagenix Vs Shakeology. The biggest difference is that Isagenix has more dietary options, like shakes that are gluten-free, soy-free, and low glycemic. Shakeology, on the other hand, isn’t gluten-free, but it does contain ingredients that don’t contain gluten. Also, Shakeology offers more flavor options. Both companies are direct-marketing companies, so they sell shakes and other products for a higher price than a store.