EMIR is the NIR imager and multiobject spectrograph being built as a common user instrument for the 10-m class GTC. Big cryogenic instruments demand a reliable design and a specific hardware and software to increase its safety and productivity. EMIR vacuum, cooling and heating systems are monitored and partially controlled by a Programmable Logic Controller (PLC) in industrial format with a touch screen. The PLC aids the instrument operator in the maintenance tasks recovering autonomously vacuum if required or proposing preventive maintenance actions. The PLC and its associated hardware improve EMIR safety having immediate reactions against eventual failure modes in the instrument or in external supplies, including hardware failures during the heating procedure or failure in the PLC itself. EMIR PLC provides detailed information periodically about status and alarms of vacuum and cooling components or external supplies.