Despite the high expectation of virtual learning environments (VLEs) to accelerate meaningful educational innovations for more interactive learning and teaching, resistance to changes exists, and innovations are fading over time. How to promote widespread and steady adoption of VLE enabled innovations remains an open question. This study uses mixed methods to examine 13 years of VLE logs, archival documents, and interviews with 51 teachers to investigate two research questions: What is the threshold stage of the institutionalisation process of VLE enabled innovation, and how does the innovation become institutionalised in the threshold stage? We found that the majority VLE enabled innovations (such as virtual classrooms and interactive quizzes) were abandoned or faded before the new or changed learning and teaching practices were fully habitualised. The empirical results show that individual cognitive divergence and collective consensus could promote habitualised institutional leverage through a threshold process, namely, meaning-making. These findings extend our understanding of the cognitive mechanism, and we suggest that universities provide continuous facilitating and teacher support, both on technological use and pedagogical design, to help teachers develop the meaning of the action as a priority. Research significance and implications to the educational transformation in the COVID-19 pandemic are discussed.