Procedural and conceptual e-scaffolding has been shown to be effective for assisting novice learners in understanding new concepts. Its integration with modelling instructions (E-MI) raises expectations for improving scientific reasoning (SR) in students whose level is still a concern in Indonesia. A quasi-experimental study was conducted to find out if there was a difference between e-scaffolding and a regular modelling instruction (MI) class; how integration affected the shift in students' SR levels; and the effect size on students' SR in physics. A total of 70 first-year high school science class students in East Java, Indonesia participated in this study, and were randomly divided into two groups with different treatments. The experimental group with E-MI (n = 35) and the control group with MI (n = 35) received a 15-item scientific reasoning test ([alpha] = 0.828), and the data were analysed by t-test. The difference in SR between the EMI and MI group was found to be statistically significant. As a result, students who learned physics through E-MI exhibited higher levels of SR compared to students who took only an MI course. In the E-MI group, elevating the SR level for students at the transitional level was relatively easier than for students at the concrete level. Integrating procedural and conceptual e-scaffolding in modelling instructions also had a large influence on students' SR in physics. In conclusion, the findings of this study underscored the importance of technology in education. E-scaffolding facilitated the augmentation of students' SR levels, excluding the operationally concrete SR levels.