Writing for scientific paper might seem a frightening task to a new researcher. This research aims at assessing the preference of Indonesian university students in Mendeley reference manager for scientific writing. This research applied survey research to find data to decide the straightforward characteristics of Indonesian Mendeley community in scientific writing. The researchers analyzed the data by using one-way tables focusing on the preferences of Mendeley features, which include citing as you read, annotate as you read, organizing your content, and access your research anywhere. This research indicated that Indonesian university students prefer to use Mendeley Word plugin, but then rather inexperienced with Bibtex export with LaTeX that entails more strict skill. This research also showed many Indonesian university students were reasonably skilled importing papers either from desktop or website. This study also indicated that Indonesian university students prefer to access Mendeley using a mobile device. This research recommends the government and scholars as well as academician to increase the scientific publication trend, with policy support as an authorized control. Mendeley could be beneficial for learners' literacy development through mostly two Mendeley features entails "cite as you read" and "annotate as you read." Mendeley as one the Reference Managers encompasses a medium to facilitate student for automatic citing and referencing the sources properly. However, the scientific environment requires a serious awareness by related stakeholders to use Mendeley wisely.