Introduction Assessing newborn infants at risk for early-onset sepsis (EOS) is a common clinical task conducted by pediatricians. A change in the internal protocol for managing neonates at risk was implemented in 2016. Unlike the previous protocol, which determined laboratory testing in asymptomatic newborns in the presence of one risk factor (RF) for sepsis; the new protocol advocates the screening in the presence of at least two RF. The purpose of this study was to characterize newborns at increased risk for EOS before and after the implementation of a diagnostic/treatment protocol. Methods Retrospective analysis of asymptomatic newborns with RF to EOS who had laboratory testing performed at perinatology department in a central hospital in north of Portugal before and after the protocol was reviewed (2016), in the years 2015 and 2017, respectively. Patients were divided in two groups: preprotocol (2015) and postprotocol (2017), according to the date of admission. Results A total of 361 newborns were enrolled, 296 (82%) pre-protocol and 65 (18%) post-protocol. There was a significant raise in the number of preterm newborns (9.5 versus 30.8%, pre- and post-protocol, respectively; p < .001), with similar other sociodemographic characteristics. There were 36 positive laboratory screenings at 12 h of life and 8.6% were transferred to the neonatology department, without differences between the groups (p = .250 and p = .488). All presented a favorable outcome, without differences in the number of readmissions in the first month of life (p = .204). Discussion The modification of the approach protocol has led to a significant decline in the laboratory testing performed, minimizing newborn pain, unnecessary antibiotic exposure and costs, without increased risk of readmission for sepsis.