Skipping breakfast might have an impact on cognitive functions, such as interference, which is a basic capacity of executive functions that denotes the possibility of controlling an automated response. This study aimed to analyze the association between nutritional quality of breakfast and cognitive interference in a sample of university students. A cross-sectional study was conducted, a total of 422 students between 18 and 25 years participated. Cognitive interference was assessed with the Stroop Test. Breakfast was assessed with a questionnaire assigning a score for each serving of each food group that was consumed. Logistic regression models were performed. The performance in cognitive tasks was slower in those who had a poor breakfast (32.9 ± 6 vs 29.3 ± 6 s, p < 0.050). Poor cognitive interference was greater in students with poor breakfast (53% versus 23%, p = 0.001). A slower word reading was associated with skipping vegetables (OR: 2.78, 95% CI: 0.09–2.13), and cereals (OR: 1.70, 95% CI: 1.03–2.81). Wrong color identification was associated with skipping fruits (OR: 1.55, 95% CI: 1.43–1.99) and animal protein sources (OR: 1.63, 95% CI: 1.07–2.49). Skipping fat-rich cereals was a protector factor (OR: 0.55, 95% CI: 0.36–0.85). Difficulty in the ability to inhibit interference was associated with skipping vegetables (OR: 2.72, 95% CI: 1.25–4.80) and cereals (OR: 2.65, 95% CI: 1.28–4.68). The nutritional quality of breakfast was associated with the time spent answering the Stroop test, but not with cognitive interference.