Objective: To determine the incidence of low libido in women using the levonorgestrel (LNG) subdermal implant for contraception after 12 months and to identify other adverse effects. Materials and methods: Cohort study that included women over the age of 18, with no children or prior gestations and in a stable relationship, with an LNG implant inserted at least three months before in a private teaching hospital in Armenia (Quindío), Colombia, between 2014 and 2019. Women with a history of sexual dysfunction, sexually transmitted infections in the past six months, weighing more than 89 kg and difficult to follow were excluded. Consecutive sampling was used. The characteristics of the study population were described, the cumulative incidence of low libido and the adverse effects related to the LNG subdermal implant after 12 months of follow-up were estimated. The tool used was the Female Sexual Dysfunction Index (FSFI). Descriptive statistics were applied. Results: The participants were 238 women with a mean age of 24.69 (SD ± 5.82) years. An 18.82% incidence of low libido was found. In 60.25% of the women were diagnosed with low libido in the first 6 months of follow-up. Adverse effects manifested as early as 3 months after the insertion of the implant, the most frequent being irregular bleeding (62.34%), followed by amenorrhea (38.91%) and weight gain (33.89%). Conclusions: It is important for practitioners and users to become aware of the presence of low libido disorder and the adverse events that may occur with the use of the levonorgestrel subdermal implant. Future research is required to confirm these findings and the underlying physiological cause.