Abstract Characterisation of internal atmosphere composition offers the potential to explain variability in responses of horticultural crops to modified atmosphere treatments and to quantify permeance of fruit skins to the respiratory gases. In this paper, the theoretical basis by which fruit skin permeance can be calculated from other gas exchange variables is presented. Surface chambers close to equilibrium with the fruit’s internal atmosphere were used to monitor internal atmosphere composition of sweet pepper (Capsicum annum, cv. Reflex). Physical equilibration of chamber contents over wounded fruit surface was essentially complete in less than 4 h. However, physiological drift in internal atmosphere composition meant that substantial changes continued to develop over more extensive periods. Removal of cuticle beneath the chamber was shown to be essential for equilibration of chamber contents within physiologically meaningful periods. Samples of atmosphere removed destructively from the fruit cavity consistently contained more O2 but less CO2 than samples similarly removed from the fruit flesh. Levels of CO2 were higher in samples removed directly from the flesh by syringe than in those taken from surface chambers, indicating potential for an effect of the vacuum used to take direct removal samples on sample composition. Permeance of pepper cuticle to CO2 was about ten times greater than that to O2 (∼244 and 24 pmols−1m−2 per Pa, respectively). Removal of cuticle dramatically increased permeance of the fruit surface and hastened equilibration of surface chambers with the fruit’s internal atmosphere. Surface chambers adhered over fruit surface from which the cuticle has been removed would be the most reliable means to assess composition of the atmosphere in immediate contact with the cells of pepper tissue.