Twenty-first-century teaching focuses on the standards of teaching practice to improve instruction and learning outcomes. Teachers as the key figures in school are called upon to reflect on their instructional practices and exemplify the highest standard for teaching grounded in global best practices. This study aimed to assess the teachers' instructional practices and identify challenges before and during the COVID-19 pandemic to effectively implement instructional strategies in the teaching of chemistry. The respondents were composed of 107 public Junior High School chemistry teachers in the 8th district of Cavite. The mixed-method sequential explanatory research design was used. Quantitative data were collected using the Science Instructional Practices Survey and the questionnaire on the teachers' perceptions of emergency remote teaching, while qualitative data were gathered utilizing focus group discussions, classroom observations, and virtual interviews. The findings of the study showed that chemistry teachers' instructional practices include prior knowledge and traditional instruction. Before the COVID-19 pandemic, four major themes emerged as challenges to teachers in effectively implementing various instructional strategies: learner characteristics, teacher competency, the language of instruction, and classroom management practices. Five themes were identified as challenges to teachers during the pandemic, namely, appropriate assessment strategy, feedback mechanism, technology usage and availability, parental involvement, and appropriate teaching-learning materials. The findings in this study provided valuable inputs in the development of an innovative instructional model for designing a chemistry lesson.