The current work reports the results of students' social presence in web-based discussions for their conceptual learning of organic chemistry. The results in this study were collected from the examined students-students, students-instructor, and students-learning materials interactions via the designed web-based discussion. We created an online forum known as "Universal Chemistry Network" to enhance communication among students and teachers in organic chemistry classes. The population comprises four hundred thirty-two (432) 11th-grade students studying chemistry in these combinations. However, a sample of 138 chemistry students was purposively selected from 36 secondary schools located in Kicukiro District in Rwanda. A questionnaire composed of multiple-choice and open-ended questions and a chemistry achievement test were used to collect data. The obtained data were analyzed by using descriptive statistics, inferential statistics, and interpretive analysis. The results revealed that the use of web-based discussion is a potentially effective teaching method for enhancing student-student and student-teacher interactions in organic chemistry classes. Students appreciated this teaching and learning method as it helped them to search for additional information related to the subject taught and exchange ideas, knowledge, and experiences. The web-based discussion was also found to provide the students with the potential confidence and motivation to express easily their opinions. The repeated measures ANOVA showed that web-based discussion increases students' academic performance in organic chemistry (p < 0.001, [eta]=0.406). However, there is no statistically significant difference in the mean score between males and females (p > 0.05, [eta]=0.27). The challenges faced by students during web-based discussions while learning organic chemistry were also examined.