On August, 24th 2016, the electron gun accelerated the first photo-electrons in SwissFEL up to the energy of 7 MeV, initiating the beam commissioning phase of the new SwissFEL facility. After several days of RF conditioning, the gun reached the nominal acceleration gradient of 100MV/m at an input power of 17MW with a pulse-width of 1 micro second at an operating frequency of at 2998.8 MHz. This gun has previously already been commissioned in the SwissFEL Test Facility from June until October 2014 and then relocated to the new SwissFEL facility in the forest of Würenlingen. During this period, several upgrades to the system have been carried out; The klystron and pulsed high power modulator systems have been relocated and equipped with new, improved high voltage connectors, a rectifier unit, suitable to allow 100 Hz stable operation, and a new isolation oil purification system. The RF-system has also been equipped with a new interlock system to ensure safe operation. Additionally, a new optical based reference signal system provides ultra-low phase jitter rf signals in the few femto seconds range which guarantees, together with a new sophisticated low level RF system, stable operation and synchronization with all other subsystems. The low level RF system is well integrated into the EPICS control system and delivers detailed beam synchronous data for every RF pulse.