Although Indonesia’s electrification ratio reached 99.2% in 2020, it has shown stagnating electrification since 2018. This is because most of the remaining areas that need to be electrified are remote and have unique characteristics that hamper implementation of microgrids for providing energy access. Furthermore, not only the deployment but also the long-term sustainability of microgrids is crucial for ensuring continuity of energy access. This paper aims to investigate the scaling and sustainability challenges of remote microgrid development in Indonesia by analyzing microgrids in the Maluku and North Maluku provinces. This study is a two-part publication; the first part focuses on identifying challenges in Indonesia’s remote microgrid development, while the second part focuses on potential technology solutions. In the first part, an assessment of energy access within a multi-tier framework was conducted, which was then analyzed using a multi-dimensional (institutional, social, technical, economic, environmental, and policy) approach adapted from the literature. The framework was expanded by mapping the challenges onto specific phases of the microgrid development, which is intended to be helpful for the parties involved in specific phases. It is shown that the challenges related to unclear land status, lack of social engagement, preliminary survey, technical and practical knowledge, and O&M procedures—especially for remote microgrids with renewable energy sources—are the most prominent issues. Additionally, issues caused by electrical events and environmental conditions such as relatively humid and high-temperatures, and uncontrolled vegetation, rodents, insects, and lizards are often found. Furthermore, a high-level technological outlook to address some of these issues is presented.