The ongoing pandemic calls for dire measures as education transitions to online classes. Although the online set-up has its benefits, miscommunication drifts in the air because of and not limited to unstable internet connection, lack of face-to-face communication, expectations of teachers to students and vice versa, especially in the Science, Technology, Engineering, and Mathematics (STEM) strand. With this, the researchers aim to 1) identify the types of miscommunication encountered by CSA-Makati Grade 11 students in learning STEM-based specialized subjects; 2) determine the effects of miscommunication in learning STEM-based specialized subjects to a Grade 11 student’s general average; and, 3) discern the needed actions for teachers and students to employ to prevent future miscommunication in learning STEM-based specialized subjects. To answer the research problems and objectives, a series of scales, including the Binary Scale, Likert Scale, and open-ended questions that collects their demographics and general averages will be used, revolving around different variables as to why miscommunication is accumulated.