Considering the symptoms of (chemo) radiotherapy and the reduction in food intake in head and neck cancer (HNC) patients, this study aimed to investigate the association between treatment time points and oral nutritional supplementation (ONS) on dietary intake to estimate the frequency of energy and nutrient inadequacy, and also to evaluate body weight changes (BWC). Dietary intake data of 65 patients were obtained from 24-h dietary recalls and prevalence of inadequacy was calculated before or at the beginning (T0), in the middle (T1), and at the end of treatment (T2). BWC were calculated as the weight difference considering the previous weight reported and/or measured. Energy and macronutrient intake decreased in T1 and then improved in T2 (p < 0.001 for both). Micronutrient intake increased during treatment due to ONS use, but still presented a high probability of inadequate intake. In particular, calcium, magnesium, and vitamin B6 showed almost 100% of probability of inadequacy for those who did not use ONS. Finally, overweight patients suffered a higher weight accumulated deficit with a delta of −15 kg compared to other BMI (body mass index) categories. Therefore, we strongly recommend initiating nutritional counseling in conjunction with prophylactic ONS prescription from diagnosis to adjust nutrient intake and minimize weight loss.