Despite consensus that preoperative nutritional assessment is of importance in the head and neck surgical oncology population, it remains unclear how exactly malnutrition is associated with perioperative morbidity especially among those undergoing microvascular surgery. We aimed to study this association to help inform preoperative risk stratification, guide the use of nutritional interventions, and ultimately help prevent malnutrition related morbidity. Database analysis. Retrospective, linked analysis of the 2011 to 2016 National Surgical Quality Improvement Program. After identifying eligible patients and stratifying according to the Nutrition-Related Index, a univariate screen of preoperative demographic and clinical covariates was performed. Subsequently, propensity score matching was utilized to control for differences in baseline covariates. Perioperative complications and mortality were then analyzed using the propensity score-matched cohorts. Among 977 identified patients, 276 (28.2%) were malnourished. Malnourished patients had higher rates of comorbidity, were more likely to actively smoke, and were more likely to have primaries in the oropharynx or hypopharynx/larynx. After propensity score matching to control for confounders, malnourished patients had higher rates of pulmonary complications (21.5% vs. 11.6%, P < .01), higher rates of bleeding or need for transfusion (56.6% vs. 43.0%, P < .01), higher rates of venous thromboembolism (3.7% vs. 0.8%, P = .03), and a higher 30-day mortality rates (3.7% vs. 0.0%, P < .01). This nationwide analysis finds that 28.2% of patients undergoing surgery for head and neck cancers with free flap reconstruction are malnourished. Malnourishment was found to be independently associated with postoperative pulmonary complications, bleeding or need for transfusion, and 30-day mortality. NA Laryngoscope, 130:375-380, 2020. © 2019 The American Laryngological, Rhinological and Otological Society, Inc.