As a democratic country undertaking a democratic transition in 1998, Indonesia has gained worldwide attention and recognition for the practice toward good democratic governance. However, the existence of a democratic government practically goes hand in hand with the domination of elites, transactional politics, or cartel politics in government, allegedly due to the absence of resilient control as a manifestation of the mechanism of checks and balances among the branches of state power. This condition thus indicates the quality of democratic practice which tends to be artificial. In the end, this condition leads to the weakening quality of the democratic transition in Indonesia, thereby deteriorating democracy. This article implements a qualitative method and focuses on the practice of checks and balances in executives, legislative, and judicial level by looking at the practice of the opposition as well as the role of parliament and the judiciary in performing its control and balancing functions. This article concludes that weak practice of the checks and balances mechanism in Indonesia could subsequently threaten the sustainability of the democratic transition in the future. In this regard, attempts such as institutionalization of the opposition, strengthening DPD, harmonization, and synchronization of supervision within the judicial power are deemed pivotal to prevent the democratic setbacks in the future.