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Recently, scholars have suggested a co-design collaboration with instructors and students to effectively implement formative assessment (FA) practices because it ensures a high-quality design that considers users’ needs, values, and goals in a specific learning context. This study examines the effect of co-designed FA practices, in which preservice science teachers (PSTs) are co-designers of FA practices, on promoting their conceptual understanding of chemistry topics in a first-year undergraduate chemistry laboratory course. Sixteen randomly selected PSTs participated in the study for two consecutive semesters. At the end of the first semester, a co-design of the FA practices was developed collaboratively with the PSTs upon the approach of conjecture mapping. Then, the second semester was devoted to examining the impact of the co-design-based FA environment on overcoming the PSTs’ alternative conceptions regarding selected four chemistry laboratory topics: thermochemistry, chemical kinetics, chemical equilibrium, acids and bases. This study employed a conversion mixed research design. To evaluate the co-design-based FA practices, PSTs’ alternative conceptions were identified through pre- and post-laboratory concept maps. The results obtained from both qualitative and quantitative data analyses showed that implementing the co-designed FA practices had a significant impact on overcoming most of the alternative conceptions held by the PSTs in all topics of laboratory investigations. This study strongly implies the inclusion of undergraduate students as active co-participants of the iterative reasoning process of the FA design to promote their understanding of chemical concepts in laboratory courses.