Internal electronic tagging is a major issue in flatfish species due to the small size of abdominal cavity. In this study, three tag types, referred to as Nonatec, nano and mini, were evaluated in three weight classes of Senegalese sole: small (0.3 g), middle (0.8 g) and large (2.0 g). Tags were injected from the blind side and fish were carefully handled to minimize sharp movements. Tag losses were 8% in the small size class, between 5.2 and 15.1% in the middle size class and 2–4% in the large size class. The mortality rates ranged between 2.0 and 15.0% with the lowest values in the large size class. No negative effects of tags on growth (tagged vs non-tagged fish using a middle size class) were found after 57 days of culture. Four additional trials using mini tags in a large size class at industrial scale validated our experimental results. With respect to morphology, no differences in the area, ellipticity and circularity were found except for a slight higher aspect ratio index in mini- and nano-tagged soles when compared with untagged fish. A longitudinal analysis of growth using the tag type, sex and tag position (anterior, medium or posterior) as fixed factors revealed a significant and strong effect of sex, with females appearing significantly heavier (13.6%) than males. In addition, the significant interactions between tag position and tag type with the time indicated a delayed growth of Nonatec-tagged fish and specimens with tags in the posterior section of abdomen. Expression analysis of stress-related genes revealed an activation of HPI axis and cellular stress defenses at 2 days just after tagging (dat) not evident at 11 dat. All these data indicate that soles can be successfully tagged at very small sizes both at experimental and industrial scales if tag type is properly selected and fish correctly handled. Moreover, sex and tag position are significant factors affecting growth that need to be controlled in longitudinal studies and selective breeding programs.