Abstract In the near future galaxy surveys will target Lyman alpha emitting galaxies (LAEs) to unveil the nature of dark energy. It has been suggested that the observability of LAEs is coupled to the large scale properties of the intergalactic medium. Such coupling could introduce distortions into the observed clustering of LAEs, adding a new potential difficulty to the interpretation of upcoming surveys. We present a model of LAEs that incorporates $\rm {Ly}α$ radiative transfer processes in the interstellar and intergalactic medium. The model is implemented in the GALFORM semi-analytic model of galaxy of formation and evolution. We find that the radiative transfer inside galaxies produces selection effects over galaxy properties. In particular, observed LAEs tend to have low metallicities and intermediate star formation rates. At low redshift we find no evidence of a correlation between the spatial distribution of LAEs and the intergalactic medium properties. However, at high redshift the LAEs are linked to the line of sight velocity and density gradient of the intergalactic medium. The strength of the coupling depends on the outflow properties of the galaxies and redshift. This effect modifies the clustering of LAEs on large scales, adding non linear features. In particular, our model predicts modifications to the shape and position of the baryon acoustic oscillation peak. This work highlights the importance of including radiative transfer physics in the cosmological analysis of LAEs.