We perform a systematic study of how the inhomogeneities in the intergalactic medium (IGM) affect the observability of Lyα emitters (LAEs) around the epoch of reionization. We focus on the IGM close to the galaxies as the detailed ionization distribution and velocity fields of this region could significantly influence the scattering of Lyα photons off neutral H atoms as they traverse the IGM after escaping from the galaxy. We simulate the surface brightness (SB) maps and spectra of more than 100 LAEs at z = 7.7 as seen by an observer at z = 0. To achieve this, we extract the source properties of galaxies and their surrounding IGM from cosmological simulations of box sizes 5–30 h−1 Mpc and then follow the coupled radiative transfer of ionizing and Lyα radiation through the IGM using crashα. We find that the simulated SB profiles are extended and their detailed structure is affected by inhomogeneities in the IGM, especially at high neutral fractions. The detectability of LAEs and the fraction of the flux observed depend heavily on the shape of the SB profile and the SB threshold (SB th) of the observational campaign. Only ultradeep observations (e.g. erg s−1 cm−2 arcsec−2) would be able to obtain the true underlying mass–luminosity relation and luminosity functions of LAEs. The details of our results depend on whether Lyα photons are significantly shifted in the galaxy to longer wavelengths, the mean ionization fraction in the IGM and the clustering of ionizing sources. These effects can lead to an easier escape of Lyα photons with less scattering in the IGM and a concentrated SB profile, similar to the one of a point source. Finally, we show that the SB profiles are steeper at high-ionization fraction for the same LAE sample which can potentially be observed from the stacked profile of a large number of LAEs.