The use of virtual laboratory simulations in various disciplines, which provide important educational benefits, has increased. Several studies show that laboratory activities, including scenario-based virtual laboratory simulation (SB-VLS), stimulate cognitive and non-cognitive skills. However, the effects of the SB-VLS when integrated into molecular biology courses, on the development of cognitive skills, such as scientific report writing skills, remain unexplored. A pre-post-test, randomized, quasi-experimental design was used. Thirty-five female students were randomly assigned to experimental or control groups. The control group (n = 17) attended a traditional lecture and video lab demonstration (VLD), while the experimental group (n = 18) participated in SB-VLS on molecular cloning. Findings revealed statistically significant differences, with large effects sizes in the SB-VLS group between pre- and post-test in intrinsic motivation (2.9 vs 3.86, p = 0.042, Cohen's d = 4.17), self-efficacy (3.31 vs 3.85, p = 0.002, Cohen's d = 1.071), and knowledge gain scales (50.93 vs 75.93, p = 0.001, Cohen's d = 1.46). Moreover, between-group effect sizes of the experimental and control groups were also large for intrinsic motivation (dppc2 = 1.441), self-efficacy (dppc2 = 0.766), and knowledge (dppc2 = 1.147), indicating that the effect of the SB-VLS was significant, which may be due to the activities and techniques used in SB-VLS to develop learning outcomes. Additionally, the SB-VLS group had statistically better lab report scores as compared to the control group (3.92 vs. 4.72, p < 0.0001). Collectively, our data show that SB-VLS is an innovative teaching strategy and an effective tool for developing non-cognitive and cognitive skills, especially scientific report writing skills.