The study aims to design a socio-scientific issues (SSIs)-based electronic learning (e-LM) design framework. It is anchored to the SSI occurrences in teaching Science at a State University in Batangas province, Philippines. This SSI-based e-LM design framework will guide the e-LM development for teaching Science socio-contextually through flexible learning. The explanatory sequential mixed method design addressed the study's goal. Initially, the existing SSIs in the science course curriculum were analyzed. Significant insights into the occurrence of existing SSIs, such as the appropriate teaching approaches, suitable teaching strategies, assessments, and e-LM design structure, were identified. The resulting least occurring SSI identified and factors affecting their existence comprised the salient features of the proposed e-LM design framework. Findings showed that lifelong learning issues, ethical issues, and sustainability issues were almost "no occurrences at all" SSIs in the analysis. These identified SSIs became the priority SSIs in e-LM design framework. Significant insights showed that flexible learning and socio-contextualization are suitable teaching approaches. Meanwhile, the teaching strategies that were found appropriate in the SSI inclusion include brain-netting, discovering scientific ideas, e-collaboration, and reflective thinking evaluation. The e-LM design framework proposed is called Brain-DeCoR e-LM Framework. Applying the proposed e-LM design framework in teaching Science will encourage science facilitators to situate priority SSIs in teaching Science. This results in creating a balance in SSI inclusion. The least occurring SSIs, which are the priority SSIs, are given into focus. Furthermore, the proposed framework will aid students in learning science beyond the content, developing their skills, and enhancing their environmental concerns and social awareness.