Peer tutoring in combination with math digital tools was employed with middle school students learning mathematics. A total of 112 students in 9th grade (14 to 15 years old) participated in the study. A pretest–posttest with control group design was used. Students worked with systems of linear equations during the experience. The effects of the intervention of peer tutoring in combination with math digital tools on students’ mathematics achievement were examined using quantitative methods. The way students in the experimental group learned and their motivation towards using digital tools compared with students in the control group were analysed qualitatively. Statistically significant improvements and a large effect size were reported for students’ mathematics achievement in the experimental group. No statistically significant differences were reported between the pretest and the posttest for the control group. The qualitative analyses revealed that students in the experimental group achieved a higher level of autonomous learning, showed a greater association of mathematical concepts, helped their peers more, did more exercises and problems than students in the control group, and enjoyed the experience.