Runaway stars are ejected from their formation sites well within molecular cores in giant dark clouds. Eventually, these stars can travel through the molecular clouds, which are highly inhomogeneous. The powerful winds of massive runaway stars interact with the medium forming bowshocks. Recent observations and theoretical modelling suggest that these bowshocks emit non-thermal radiation. As the massive stars move through the inhomogeneous ambient gas the physical properties of the bowshocks are modified, producing changes in the non-thermal emission. We aim to compute the non-thermal radiation produced in the bowshocks of runaway massive stars when travelling through a molecular cloud. We calculate the non-thermal emission and absorption for two types of massive runaway stars, an O9I and an O4I, as they move through a density gradient. We present the spectral energy distributions for the runaway stars modelled. Additionally, we obtain light curves at different energy ranges. We find significant variations in the emission over timescales of $\sim$ 1 yr. We conclude that bowshocks of massive runaway stars, under some assumptions, might be variable gamma-ray sources, with variability timescales that depend on the medium density profile. These objects might constitute a population of galactic gamma-ray sources turning on and off within years.Instituto Argentino de RadioastronomíaFacultad de Ciencias Astronómicas y Geofísicas