Communication and planning are skills expected among graduates. However, a skills deficit continues to be present among students. To address this problem, here we considered the final year project (FYP), a widely used way of working on skills in STEM degrees. Furthermore, we took into account recent research that highlights the importance of students' thoughts, beliefs, and emotions, in addition to characteristics such as self-efficacy or self-management within the learning process. Here a framework was designed around a semi-guided learning approach, with the aim of improving STEM students' skills and providing them with a work context that facilitates favorable behaviors and feelings associated with writing their FYP report. This framework, implemented in a Spanish university in Madrid, was designed to accomplish their work during restricted face-to-face work due to COVID-19. Through mixed-focus surveys, the perceptions of 55 students (male/female ratio = 4) were collected in relation to what the framework had provided them. The results showed that most of the students perceived improvement both in planning and written communication skills. The qualitative analysis also allowed us to determine the most common difficulties found among students, as well as benefits provided by the framework, among which they highlighted, greater efficiency in the writing process and help to ensure the quality of the FYP report. Our findings allow promoting beneficial results for STEM student and support the idea of considering the cognitive-emotional context of the student as a part of the environment in which to develop facilitating tools for learning and skills development.