Recommender systems are currently a suitable alternative for providing easy and appropriate access to information for users in today’s digital information-overloaded world. However, an important drawback of these systems is the inconsistent behavior of users in providing item preferences. To address this issue, several natural noise management (NNM) approaches have been proposed, which positively influence recommendation accuracy. However, a major limitation of such previous works is the disregarding of the time-related information coupled to the rating data in RSs. Based on this motivation, this paper proposes two novel methods, named SeqNNM and SeqNNM-p for NNM focused on an incremental, time-aware recommender system scenario that has not yet been considered, by performing a classification-based NNM over specific preference sequences, driven by their associated timestamps. Such methods have been evaluated by simulating a real-time scenario and using metrics such as mean absolute error, root-mean-square error, precision, recall, NDCG, number of modified ratings, and running time. The obtained experimental results show that in the used settings, it is possible to achieve better recommendation accuracy with a low intrusion degree. Furthermore, the main innovation associated with the overall contribution is the screening of natural noise management approaches to be used on specific preferences subsets, and not over the whole dataset as discussed by previous authors. These proposed approaches allow the use of natural noise management in large datasets, in which it would be very difficult to correct the entire data.