We aimed to evaluate the impact of an educational intervention on the surface cleaning and disinfection of an emergency room. This is an interventional, prospective, longitudinal, analytical and comparative study. Data collection consisted of three stages (Stage 1—baseline, Stage 2—intervention and immediate assessment, Stage 3—long term assessment). For the statistical analysis, we used a significance level of α = 0.05. The Wilcoxon and the Mann–Whitney test tests were applied. We performed 192 assessments in each stage totaling 576 evaluations. Considering the ATP method, the percentage of approval increased after the educational intervention, as the approval rate for ATP was 25% (Stage 1), immediately after the intervention it went to 100% of the approval (Stage 2), and in the long run, 75% of the areas have been fully approved. Stage 1 showed the existence of significant differences between the relative light units (RLU) scores on only two surfaces assessed: dressing cart (p = 0.021) and women’s toilet flush handle (p = 0.014); Stage 2 presented three results with significant differences for ATP: dressing cart (p = 0.014), women’s restroom door handle (p = 0.014) and women’s toilet flush handle (p = 0.014); in step III, there was no significant difference for the ATP method. Therefore, conclusively, the educational intervention had a positive result in the short term for ATP; however, the same rates are not observed with the colony-forming units (CFU), due to their high sensitivity and the visual inspection method since four surfaces had defects in their structure.