Mycobacterium tuberculosis uses the specialised ESX-1 secretion system to secrete virulence factors and potent immunogenic effectors required for disease progression. ESX-1 is a multi-subunit apparatus with a membrane complex that is predicted to form a pore in the cytoplasmic membrane. In M. tuberculosis this complex is composed of five membrane proteins: EccB1, EccCa1, EccCb1, EccD1, EccE1. In this study, we have characterised the membrane component EccE1, and we found that deletion of eccE1 leads to destabilisation of EccB1, EccCa1 and EccD1 levels as well as to the disruption of EsxA, EsxB, EspA and EspC secretion. Surprisingly, secretion of EspB was not affected by loss of EccE1.