Obesity is associated with reduced gut microbial diversity and a high rate of micronutrient deficiency. Bariatric surgery, the therapy of choice for severe obesity, produces sustained weight loss and improvements in obesity-related comorbidities. Also, it significantly alters the gut microbiota (GM) composition and function, which might have an important impact on the micronutrient status as GM is able to synthesize certain vitamins, such as riboflavin, folate, B12, or vitamin K2. However, recent data have reported that GM is not fully restored after bariatric surgery; therefore, manipulation of GM through probiotics represents a promising therapeutic approach in bariatric patients. In this review, we discuss the latest evidence concerning the relationship between obesity, GM and micronutrients, the impact of bariatric surgery on GM in relation with micronutrients equilibrium, and the importance of the probiotics’ supplementation in obese patients submitted to surgical treatment.