Increasing consumer awareness on good health has drawn the attention to health promoting natural dietary substances. However, since the organoleptic profile of foods highly influences the consumers' preference, and it is often decisive in the purchase, it is important to objectively describe and evaluate the effect of the applied bioactive ingredients on aroma. In this study, pancakes enriched with docosahexaenoic acid and anthocyanins were tested with electronic sensor array technology against control products. Samples were analyzed with an Alpha MOS FOX4000 electronic nose (EN) after 20 to 297 days of frozen storage at −20 °C. Multivariate analysis of the acquired EN data showed a strong relation between the number of days that samples were stored and the odor describing sensor signals of enriched samples (R 2 = 0.59), but the observed relation was broken in the case of control (not enriched) samples (R 2 = 0.08). When a supervised classification of enriched and control samples was done, the ratio of correctly identified samples in cross-validation was 95.1% at short-term storage (< 140 days), while the hit rate dropped to 80.4% at prolonged storage (> 140 days). This signified the existing but less intensive odor differences. The electronic nose technology was proven to be applicable in the characterization of one type of bioactive-enriched foods, while it was also useful in the monitoring of odor alterations during storage.