Abstract Background Women represent an increasingly growing share of the medical workforce in high-income countries, with abundant research focusing on reasons and implications of the phenomenon. Little evidence is available from low- and middle-income countries, which is odd given the possible repercussion this may have for the local supply of medical services and, ultimately, for attaining universal health coverage. Methods Drawing from secondary analysis of primary survey data, this paper analyses the proportion and characteristics of female physicians in Bissau, Maputo and Praia, with the objective of gaining insights on the extent and features of the feminization of the medical workforce in low- and middle-income settings. We used descriptive statistics, parametric and non-parametric test to compare groups and explore associations between different variables. Zero-inflated and generalized linear models were employed to analyse the number of hours worked in the private and public sector by male and female physicians. Results and discussion We show that although female physicians do not represent yet the majority of the medical workforce, feminization of the profession is under way in the three locations analysed, as women are presently over-represented in younger age groups. Female doctors distribute unevenly across medical specialties in the three cities and are absent from traditionally male-dominated ones such as surgery, orthopaedics and stomatology. Our data also show that they engage as much as their male peers in private practice, although overall they dedicate fewer hours to the profession, particularly in the public sector. Conclusions While more research is needed to understand how this phenomenon affects rural areas in a broader range of locations, our work shows the value of exploring the differences between female and male physicians’ engagement with the profession in order to anticipate the impact of such feminization on national health systems and workforces in low- and middle-income countries.