This paper presents the design and implementation of a low-cost Supervisory Control and Data Acquisition system based on a Web interface to be applied to a Hybrid Renewable Energy System (HRES) microgrid. This development will provide a reliable and low-cost control and data acquisition systems for the Renewable Energy Laboratory at Universitat Politècnica de València (LabDER-UPV) in Spain, oriented to the research on microgrid stability and energy generation. The developed low-cost SCADA operates on a microgrid that incorporates a photovoltaic array, a wind turbine, a biomass gasification plant and a battery bank as an energy storage system. Sensors and power meters for electrical parameters, such as voltage, current, frequency, power factor, power generation, and energy consumption, were processed digitally and integrated into Arduino-based devices. A master device on a Raspberry-PI board was set up to send all this information to a local database (DB), and a MySQL Web-DB linked to a Web SCADA interface, programmed in HTML5. The communications protocols include TCP/IP, I2C, SPI, and Serial communication; Arduino-based slave devices communicate with the master Raspberry-PI using NRF24L01 wireless radio frequency transceivers. Finally, a comparison between a standard SCADA against the developed Web-based SCADA system is carried out. The results of the operative tests and the cost comparison of the own-designed developed Web-SCADA system prove its reliability and low-cost, on average an 86% cheaper than a standard brandmark solution, for controlling, monitoring and data logging information, as well as for local and remote operation system when applied to the HRES microgrid testbed.