In the peer instruction (PI), students are provided with conceptual questions to help them resolve misconceptions about a subject matter. Although there are different versions of PI, it is generally designed as follows: First, students individually provide responses to the given multiple-choice questions. Second, they discuss their answers with classmates and then individually provide responses again to the same questions. In the last step, instructors provide explanations on the solutions. The questions are usually presented to the students via a blackboard, a projector or in oral form. Students can provide their answers showing hands, writing on forms, and using handheld computers, electronic voting systems or classroom response systems. The literature on PI suggests that the use of response systems with technological possibilities have some advantages on students’ learning. In this context, the purpose of this study was to examine the effect of two different methods used in the question-answer process of PI on preservice science teachers’ (PSTs) mathematics achievements. In Spring 2016 semester, 44 PSTs, who have been attending to a general mathematics course, participated in the study. In the beginning of the study, they were given a test on the integral topics. Next, they were randomly divided into two equally achieving groups based on the test results. Later, in both groups, two students, one high and one low achieving, randomly selected to form a subgroup. Each week, two groups attended together to a two-hour general mathematics class. Following, one group attended to a two-hour PI session in which they worked on computers. Whereas, the second group attended to a paper-pencil based two-hour PI session in which a projector was used in presenting questions, and the PSTs provided their responses using a standard paper form. A total of 10 weeks PI classes are planned for both groups. The data collection process is still ongoing. During the last week, each group will be given the same achievement test. The post-test results of the two groups will be compared with pretest scores to understand the effect of the two different methods used in the question-answer process.