Abstract Background This study examined whether infants aged 0–3 months exhibited long-term effects of using a moisturizer skincare intervention and whether a short-term skin problem resulted in the subsequent development of food allergies or atopic dermatitis (AD) until the age of 2 years. Methods This study was a follow-up of a completed randomized control trial (RCT) of moisturizer skincare for infants aged 0–3 months. A self-reported questionnaire was mailed to the parents of children aged 1–2 years who had participated in the RCT. Data were analyzed using a Chi square test, by intention to treat analysis, and by multiple logistic regression. Results Of 155 infants, 22 (14.2%) and 28 (18.1%) had food allergies and AD/eczema until 2 years of age, respectively. No significant difference was seen in food allergies or AD between the group that received moisturizer skincare intervention and the control group. On the contrary, food allergies until 2 years of age were significantly associated with short-term (4–7 days) and long-term (more than 7 days) body skin problems occurring in the first 3 months of life, a family history of AD, and the time of starting complementary food. High value of face transepidermal water loss at 3 months of age was also associated with food allergies. Moreover, a short duration of severe diaper dermatitis during the first 3 months, a family history of AD, and being male were significantly associated with AD/eczema until the age of 2 years. Conclusions After adjusting for family history of AD, a short-term skin problem in the first 3 months of life was significantly associated with the development of food allergies or AD/eczema until the age of 2 years. Prevention or prompt treatment of skin problems in newborns is essential for preventing future allergic diseases. Trial registration This was a follow-up study conducted 2 years after the completed RCT of a moisturizer skincare intervention for early infants, which was registered in the University Hospital Medical Information Network Clinical Trials Registry (UMIN000013260)