It has been shown that Spatial Skills is an important attribute and characteristic that every person interested in Science, Technology, Engineering and Math (STEM) must have, but also has a direct relationship with the success rates of first-year university engineering students. The purpose of this research is to analyze the levels of Spatial Skills that first-year Civil Engineering students at a Peruvian university have and determine the improvement of these levels through a short training based on Augmented Reality (AR) and compare it with academic performance. Sixty-two students were recruited out of a total population of 134 and the experimental and control group consisted of 31 students each. It was considered the Spatial Relationships and the Spatial Visualization components to be measured with the Mental Rotation Test and Differential Aptitude Test. To measure academic performance, the grading data of four subjects were used. After training, a statistically significant improvement in the Spatial Skill levels of the experimental group was evidenced. Regarding academic performance, there has been an improvement in students who have undergone specific training to improve their spatial skills. The conclusion is that a short and specific training based on AR not only improves Spatial Skills but also helps the academic performance in first-year engineering subjects.