Augmented reality is one of the technologies that will impact teaching and learning. When augmented reality is applied in an educational setting, it can provide a superior learning environment because educators can add specific virtual information to enrich the existing learning materials or to create new learning materials that integrate the environment. Therefore, discussions on augmented reality applications for learning can be vastly found in the literature. Each application utilizes the resources available by using approaches appropriate for the learning outcome in question. The key problem with achieving learning outcome in analyzing group one elements in a periodic table is that some students have difficulties in visualizing an atom and what more to relate them with reactivity. The objective of this paper aims to design and develop a learning application that supports science, technology, engineering, and mathematics (STEM) education based on guided discovery learning to assist the students through questions based on exposure to various evidence via augmented reality. This application incorporates the use of a 3D model of atoms and video of real experiments. Action research is used to solve an existing problem in a selected school. The application was evaluated by 25 students aged 16 years in a secondary school in Malaysia and has proven to be useful to improve the students' marks in tests conducted at the end of the application usage. The students can get many benefits from using the augmented reality based application because it supports Education 4.0 like flexibility in teaching and learning where learning is freed for the limitation of time, place, and pace of study.