Multidrug resistance, severe side effects, and high cancer treatment costs are still well-known issues and remain an open challenge. These factors reduce the therapy's efficiency and safety, seriously affecting human health. Developing therapeutic approaches based on plant extracts, especially based on essential oils with cytotoxic and antioxidant properties, could be of efficacious strategies. This work incorporated Thymus capitatus essential oil (TEO) in liposomes. Thymus capitatus is a plant native to the northern region of Albania and found specifically in the Mediterranean region. TEO has several biological activities and cytotoxic properties. Due to its volatility, poor solubility, and chemical instability, however, its applicability is restricted. Incorporation into liposomes enables its effective use because the exposure time to the active compounds can be extended, increasing its efficacy against colorectal cancer cell lines, as highlighted in in vitro studies. TEO demonstrated detectable cytotoxic action against HT-29 colorectal cancer cells, and this action could be enhanced by applying various formulations of TEO-loaded liposomes to this cell line. Among the tested nanosystems, TEO-Phospholipon 90H liposomes showed more significant cytotoxic effects than TEO-Lipoid S100 liposomes and TEO-Phospholipon 85G liposomes. TEO-Phospholipon 90 H liposomes also maintained its physicochemical stability for six months at 25 °C. This research suggests that TEO, particularly when encapsulated in TEO-Phospholipon 90 H liposomes, may offer a promising therapeutic approach. However, these findings are based on in vitro studies and further in vivo research is needed to validate the efficacy and safety of this approach in clinical settings.