Many studies in the field of chemical education have emphasized the fact that students at secondary level have considerable difficulties in mastering organic chemistry contents. As a result, they choose to learn these contents in a "rote" way. Taking this fact into consideration, the first aim of our study was to help students in overcoming the aforementioned difficulties by applying new instructional tools--systemic synthesis questions [SSynQs]. To achieve the aim of our research, an experiment with two parallel groups was conducted. The experimental group was taught using [SSynQs] and the control group was taught using a traditional approach. The study included 65 students, 41 males, and 24 females, aged between 17-18 years. All the students attended the same high school and were taught by the instructions of the same teacher. The results showed that students from the experimental group achieved higher scores on the final testing than students from the control group. This confirmed the fact that application of [SSynQs] in the educational process improves students' meaningful learning in organic chemistry domain. Additionally, after conducting an exploratory factor analysis of the obtained data, [SSynQs] were characterized as highly effective tools for assessing students' meaningful understanding. Furthermore, our study has highlighted and connected two applications of [SSynQs] in the chemistry educational process. Firstly as an instructional tool and secondly as an assessment tool. The important task for future research would be to evaluate a third application of [SSynQs] as a diagnostic tool.