Patients with cancer deal with problems related to physical, psychological, social, and emotional functions. The aim was to investigate malnutrition defined by the Global Leadership Initiative on Malnutrition (GLIM) criteria in relation to health-related quality of life, anxiety, and depression in patients with head and neck cancer. This was a prospective observational research study with 273 patients followed at the start of treatment, seven weeks, and one year. Data collection included nutritional status and support, and the questionnaires: European Organization for Research and Treatment of Cancer Head and neck cancer module (EORTC QLQ-H&N35) and the Hospital Anxiety and Depression Scale (HADS). Malnutrition was defined using the GLIM criteria. The study showed that patients with malnutrition had significantly greater deterioration in their health-related quality of life at seven weeks. On a group level, health-related quality of life was most severe at this time point and some scores still implied problems at one year. Significantly, more patients reported anxiety at the start of treatment whereas significantly more patients reported depression at seven weeks. Over the trajectory of care, the need for support often varies. Psychosocial support is imperative and at the end of treatment extra focus should be put on nutritional interventions and managing treatment-related symptoms to improve nutritional status and health-related quality of life. In the long-term, head and neck cancer survivors need help to find strategies to cope with the remaining sequel.