Considering the results of research on the benefits and difficulties of peer review, this paper describes how teaching faculty, interested in endorsing the acquisition of communication and critical thinking (CT) skills among engineering students, has been implementing a learning methodology throughout online peer review activities. While introducing a new methodology, it is important to weight the advantages found and the conditions that might have restrained the activity outcomes, thereby modulating its overall efficiency. Our results show that several factors are decisive for the success of the methodology: the use of specific and detailed orientation guidelines for CT skills, the students' training on how to deliver a meaningful feedback, the opportunity to counter-argument, the selection of good assignments' examples, and the constant teacher's monitoring of the activity. Results also tackle other aspects of the methodology such as the thinking skills evaluation tools (grades and tests) that most suit our reality. An improved methodology is proposed taking in account the encountered limitations, thus offering the possibility to other interested institutions to use/test and/or improve it.