We propose a joint experimental and theoretical approach to measure the self-diffusion in a lasercooled trapped ion cloud where part of the ions are shelved in a long-lived dark state. The role of the self-diffusion coefficient in the spatial organisation of the ions is deciphered, following from the good agreement between the experimental observations and the theoretical predictions. This comparison furthermore allows to deduce the temperature of the sample. Protocols to measure the self-diffusion coefficient are discussed, in regard with the control that can be reached on the relevant time scales through the dressing of the atomic levels by laser fields.