This qualitative case study explores the development of pre-service science teachers’ (PSTs) understanding of Socio-Scientific Issues (SSI) instruction. The study utilized a conceptual framework of SSI-based instruction and a three-phase approach involving co-designing solutions, co-designing curriculum materials, and co-teaching classes. Primary data sources included PSTs’ interviews and reflective journals, while artifacts, field notes, and curriculum materials served as secondary data sources. Thematic analysis was used to analyze the data of six PSTs in a teacher preparation program. We found that the PSTs’ understanding of SSI instruction was enhanced in 12 features of three core aspects: design elements, learner experiences, and teacher attributes. “Engaging in higher-order practices” was the most prominent feature, observed across all three phases. The three-phase approach played a crucial role in promoting PSTs’ understanding of SSI instruction, with each phase guiding their understanding in distinct ways. Particularly, the co-designing solutions phase facilitated the development of PSTs’ “awareness of the social considerations associated with the issue”. While the co-designing curriculum materials phase was effective in promoting their understanding of “scaffolding for practice: providing scaffolding for higher-order practices. “The co-teaching classes phase played a crucial role in facilitating their understanding of “willingness to position oneself as a knowledge contributor rather than the sole authority”.