© 2016, Springer Science+Business Media Dordrecht.Research in socioscientific issue (SSI)-based interventions is relatively new (Sadler in Journal of Research in Science Teaching 41:513–536, 2004; Zeidler et al. in Journal of Research in Science Teaching 46:74–101, 2009), and there is a need for understanding more about the effects of SSI-based learning environments (Sadler in Journal of Research in Science Teaching 41:513–536, 2004). Lee and Witz (International Journal of Science Education 31:931–960, 2009) highlighted the need for detailed case studies that would focus on how students respond to teachers’ practices of teaching SSI. This study presents case studies that investigated the development of secondary school students’ science understanding and their socioscientific reasoning within SSI-based learning environments. A multiple case study with embedded units of analysis was implemented for this research because of the contextual differences for each case. The findings of the study revealed that students’ understanding of science, including scientific method, social and cultural influences on science, and scientific bias, was strongly influenced by their experiences in SSI-based learning environments. Furthermore, multidimensional SSI-based science classes resulted in students having multiple reasoning modes, such as ethical and economic reasoning, compared to data-driven SSI-based science classes. In addition to portraying how participants presented complexity, perspectives, inquiry, and skepticism as aspects of socioscientific reasoning (Sadler et al. in Research in Science Education 37:371–391, 2007), this study proposes the inclusion of three additional aspects for the socioscientific reasoning theoretical construct: (1) identification of social domains affecting the SSI, (2) using cost and benefit analysis for evaluation of claims, and (3) understanding that SSIs and scientific studies around them are context-bound.