Breastfeeding rates remain extremely low in Greece and women with gestational diabetes mellitus and hypothyroidism may experience additional difficulties. The aim of the study was to investigate the effect of a structured individualized lactation educational intervention by a midwife on increasing breastfeeding rates in women with endocrine disorders and low-risk women compared to women receiving standard care, 24 months after delivery. Two-hundred women made up the study population. Half of them were experiencing endocrine pregnancy disorders and 100 women constituted the low-risk pregnancy standard care control group. Women who were breastfeeding exclusively were significantly higher in the midwifery intervention group with endocrine disorders, namely breastfeeding continued at four months (breastfeeding: 20% vs. 12%, exclusive breastfeeding: 50% vs. 26%, p = 0.0228), and at six months after childbirth (breastfeeding: 54% vs. 28%, exclusive breastfeeding: 32% vs. 12%, p = 0.0011), compared to the standard care control group with endocrine disorder. The low-risk midwifery intervention group breastfed at four months (22% vs. 14%, p = 0.0428) and at six months (52% vs. 26%, p = 0.0018) at higher rates compared to the standard care control group. In addition, exclusive breastfeeding was significantly higher in the low-risk midwifery intervention group at four months (46% vs. 20%, p = 0.0102) and six months (38% vs. 4%, p < 0.0001) compared to the standard care control group. This study was the first attempt of a structured midwifery breastfeeding education in Greece and its major contribution reflects a significant positive impact on breastfeeding rates in terms of duration and exclusivity in women with gestational endocrine disorders as well as in low-risk women, and could possibly be applied and instituted in everyday clinical practice to increase the low breastfeeding rates in Greece.