Background/Objectives: Hematopoietic cell transplantation (HCT) is a curative treatment for various hematological diseases but can lead to complications which increase malnutrition risk, particularly in allogeneic transplantation patients. This study evaluates the nutritional status evolution of patients undergoing HCT during hospitalization and follow-up. Methods: This retrospective observational study included 365 patients, divided into two groups: 134 underwent allogeneic HCT, while 231 underwent autologous transplantation or CAR-T therapy. Nutritional status was evaluated using Body Mass Index (BMI), Malnutrition Universal Screening Tool (MUST), and Global Leadership Initiative on Malnutrition (GLIM) criteria at four-time points: hospital admission, discharge, two-week follow-up, and one-month follow-up. Non-relapse-related complications were assessed based on hospital readmissions and reports during follow-up visits. Results: Patients experienced significant nutritional deterioration, with decreases in Body Mass Index (BMI) (p < 0.001) and increases in Malnutrition Universal Screening Tool (MUST) (p < 0.001) and Global Leadership Initiative on Malnutrition (GLIM) scores (p < 0.001), particularly among allogeneic transplant recipients (p = 0.025). Severe malnutrition or high malnutrition risk at discharge correlated with increased hospital readmissions during the follow-up (p = 0.024). Conclusions: The observed decline in nutritional status and its associated complications highlight the necessity of multidisciplinary interventions, such as nutritional prehabilitation programs and nutritional support protocols, to enhance clinical outcomes and reduce complications in HCT patients.