Malnutrition is prevalent in surgical patients and leads to comorbidities and a poorer postoperative course. There are no studies that compare the clinical outcomes of implementing a nutrition screening tool in surgical patients with standard clinical practice. An open, non-randomized, controlled study was conducted in general and digestive surgical hospitalized patients, who were either assigned to standard clinical care or to nutrition screening using the Control of Food Intake, Protein, and Anthropometry (CIPA) tool and an associated treatment protocol (n = 210 and 202, respectively). Length of stay, mortality, readmissions, in-hospital complications, transfers to critical care units, and reinterventions were evaluated. Patients in the CIPA group had a higher Charlson index on admission and underwent more oncological and hepatobiliary-pancreatic surgeries. Although not significant, a shorter mean length of stay was observed in the CIPA group (−1.48 days; p < 0.246). There were also fewer cases of exitus (seven vs. one) and fewer transfers to critical care units in this group (p = 0.068 for both). No differences were detected in other clinical variables. In conclusion, patients subjected to CIPA nutrition screening and treatment showed better clinical outcomes than those receiving usual clinical care. The results were not statistically significant, possibly due to the heterogeneity across patient groups.