Malaysia, a middle-income country aiming for high-income status, has been experiencing a troubling decline in domestic patent output since 2014. This trend remains largely unnoticed and unexplained. Malaysia’s persistent middle-income trap is associated with weak innovation capacity and declining patent activity suggests that the country is unable to transform itself into a knowledge-based economy. To uncover the patent trend in Malaysia and the variance of patenting activities, this study uses patent data from the Intellectual Property Corporation of Malaysia (MyIPO) as a proxy for domestic inventive activity in the country. The Triple Helix model and a regional perspective contributes to the explanation of our spatial and statistical descriptions of Triple Helix actors (government, industry, and academia) in Malaysia’s domestic patenting applications. Our findings reveal a geographic divergence: while patenting in the country’s largest agglomeration, Klang Valley, have dropped by 16.2% from 2018 to 2023, other more urban states like Penang and Johor have seen patent applications increase by 67.6% and 44.4%, respectively in the same time frame. This geographic heterogeneity highlights the growing role of regional innovation systems and the potential impact of regional-level policies. Our analysis of patents reveals two main trends. The first is geographic divergence of patenting activity – one that moves away from the Klang Valley. The second is changes in the patenting trend in universities and government-affiliated institutions.  Our results suggest that while public sector research appears to act as a catalyst for increased industry patenting activity, Malaysia’s experience in the 2010s indicates that efforts to stimulate industry research through investments and incentives were insufficient to effectively prime industrial innovation, which subsequently declined as policy support and investment in public sector research were reduced.