Objective Cocoa has been highlighted as a food with potential benefits to human health because of its polyphenol content. However, few studies show the contribution of cocoa and chocolate products in polyphenol intake. The aim of this work was to develop a food frequency questionnaire (FFQ) for evaluating the intake of food products containing cocoa (C-FFQ). Methods A sample of 50 university students was recruited to complete the 90-item questionnaire, a validated questionnaire (called here European Food Safety Authority [EFSA]-Q) as well as a 24-hour dietary recall (24 HDR). Spearman correlation test, Bland-Altman plots, and quintile classification analysis were conducted together with the Wilcoxon test and descriptive statistics. Results Significant correlations between the C-FFQ and the EFSA-Q for the most common cocoa/chocolate products were observed (P < 0.05), as well as between data from the C-FFQ and 24 HDR (P < 0.05). However, a number of cocoa/chocolate products frequently consumed by the participants were detected by the C-FFQ and 24 HDR which were not included in the EFSA-Q. According to the C-FFQ, chocolate bars were the main source of cocoa in university students, but dairy products also provided an important amount of cocoa. Conclusion The developed C-FFQ questionnaire can be considered as a valid option for assessing the consumption frequency of cocoa/chocolate-derived products, thereby allowing the evaluation of cocoa polyphenol intake in further studies.