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Atopic dermatitis (AD) is a chronic eczematous inflammatory disease that may arise from environmental, genetic, and immunological factors. Despite the efficacy of current treatment options such as corticosteroids, such approaches are mainly focused on symptom relief and may present certain undesirable side effects. In recent years, isolated natural compounds, oils, mixtures, and/or extracts have gained scientific attention because of their high efficiency and moderate to low toxicity. Despite their promising therapeutic effects, the applicability of such natural healthcare solutions is somewhat limited by their instability, poor solubility, and low bioavailability. Therefore, novel nanoformulation-based systems have been designed to overcome these limitations, thus enhancing the therapeutic potential, by promoting the capacity of these natural drugs to properly exert their action in AD-like skin lesions. To the best of our knowledge, this is the first literature review that has focused on summarizing recent nanoformulation-based solutions loaded with natural ingredients, specifically for the management of AD. We suggest that future studies should focus on robust clinical trials that may confirm the safety and effectiveness of such natural-based nanosystems, thus paving the way for more reliable AD treatments.