The integration of big data into the business process is a crucial aspect of the Integrated Information System (IIS). This study aims to examine how organizations integrate big data into IIS and the impact on business performance. A qualitative case study method was conducted in an Indonesian transportation company. Thematic analysis was employed to analyze the data that emerged during the in-depth interview. This study has answered how big data usage in IIS is able to produce the data analytics process needed by the company to support operational and strategic decision-making. The IIS integrates three key systems in organization, e-ticketing system, GPS data management system, and SAP, to analyze internal and external data. The findings highlight the important issue that need to be addressed by organization to implement affective IIS: (1) the design of IIS according to objectives and needs, (2) access authorization, (3) GPS data usage integration into business process, (4) facility development and training. The insights derived can potentially provide valuable direction for managers in organizations to fully utilize the potential of big data, which could lead to the improvement in business performance through big data analytics usage in IIS, increasing operational process, revenue, and cost efficiency.