The literature widely reports that pre-service teachers repeatedly demonstrate inadequate argumentation skills. Through a mixed-methods research approach, this study investigated the effectiveness of a holistic online scaffolding design for guiding the development of pre-service teachers’ argumentation skills. Participants were randomly assigned to either a control or experimental group and then applied argumentation skills to solve case-based problem scenarios on teaching methods for two weeks. The experimental group had a significant improvement in the following argumentation skills: evidence, alternative theory, and counterargument. Qualitative data collected shows diverse metacognition concerning argumentation skills within experimental group. This study suggests that embedding a holistic online scaffolding approach into teacher training programs for the development of argumentation skills offers meaningful learning opportunities for pre-service teachers.