Background: Current methods for electronic health record (EHR) storage in technically constrained clinical scenarios prove to be inefficient and limit the implementation of real-time analytics for timely monitoring of clinical performance measures. Such limitation arises significant challenges for concurrent communication protocols between stored EHR and data analytics engines, thus requiring highly demanding specifications for data warehousing in the context of limited time, resources, and technical staff. Objective: This work aims to present the development of a EHR-driven data collection workflow for healthcare analysis in the clinical and research context that enables real-time decision making and follow-up inside complex medical institutions. Methods: REDCap was integrated with the primary clinical information system to improve traditional data collection and EHR storage with low technical requirements for online data warehousing and automatic updates, interfacing with a relevant data visualization and analytics engine.ResultsWeb-based computation and real-time monitoring of customizable assessment variables from longitudinal EHR, for generating and displaying clinical performance measure sets via interactive visualization dashboards. Conclusions: The application of these processes allows us to overcome limitations given by technical restrictions of the EHR, achieving real-time access, with precision and timeliness, to relevant clinical and administrative information for making managerial decisions.