Diet has a fundamental role in the homeostasis of bodily functions, including the skin, which, as an essential protective barrier, plays a crucial role in this balance. The skin and intestine appear to share a series of indirect metabolic pathways, in a dual relationship known as the “gut-skin axis”. Hence, the gut-skin axis might be receptive to modulation via dietary modification, where probiotics can be included, thus representing a potential therapeutic target in inflammatory skin diseases, such as atopic dermatitis (AD), in order to control and/or ameliorate symptoms. Kefir is one of the most ancient fermented foods, with probiotic characteristics that have been associated with a wide variety of health-promoting benefits, and it presents a microbiological diversity that makes its application as a probiotic in the gut-skin relationship of the utmost interest. However, the impact of a diet containing kefir on skin health has yet to be reported in scientific literature. This study aimed to assess the impact of the intake of homemade kefir in the skin of healthy and atopic volunteers. The intervention resulted in a boost on barrier function in both skin types verified only in the respective kefir intake groups. An improvement in the degree of severity of AD was also confirmed for the kefir intake group. Atopic individuals may benefit from kefir intake, especially in regard to their skin hydration. Finally, the effects observed on skin barrier function in this study probably culminate from the effects of all the ingredients in kefir, including the complex microbiota, its metabolites and macro- and micronutrients resulting from the fermentation. This work opens the way for more advanced research on the impact of the probiotic kefir on cutaneous health, further clarifying its mechanism of action namely via gut-skin axis.