The Jupiter Icy Moons Explorer (Juice) embarked in 2023 on a 8-year interplanetary journey to Jupiter and its icy moons. The Submillimetre Wave Instrument (SWI) is one of the ten science instruments aboard the spacecraft. SWI is a sophisticated and first-of-its-kind payload visiting the outer solar system, featuring dual-band tunable receivers, two independent pointing mechanisms, and spectrometers capable of high resolution (up to a resolving power of 10<sup>7</sup>). It is designed to support the diverse science objectives of the Juice mission targeting Jupiter's middle atmosphere, icy-moon's exospheres as well as near sub-surface thermophysical properties. For this purpose the Juice mission adopts a complex trajectory tour within the Jovian system, which further necessitates a sophisticated, mission-driven operations concept for SWI. This presents significant planning, operations and commanding challenges which are described in this paper in the context of the Lunar and Earth Gravity Assist (LEGA). After the development and ground calibration of the instrument, the SWI Team has designed a comprehensive calibration strategy applicable during the Cruise Phase of Juice. Among the various opportunities for calibration, including the Near-Earth Commissioning Phase and more than ten Payload Checkout Windows, the LEGA offers the means not only to improve the calibration of the instrument, but also to validate the operational strategy of future icy moon flybys.