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Background: Higher intensity and longer duration of breastfeeding is associated with protection against type 2 diabetes development. While exclusive breastfeeding is optimal, women with gestational diabetes mellitus (GDM) have lower exclusive breastfeeding rates than non-diabetic women. While women with GDM have expressed that they feel that their milk “comes in” late, there is limited biochemical validation of their perception and a lack of information regarding the difference in metabolite composition of colostrum which may influence the transition to lactogenesis II. Methods: Researchers conducted a prospective case-control pilot study involving the comparison of metabolite concentrations and maternal perception of milk “coming in” between postpartum women with GDM and without GDM. Results: There were lower concentrations of lactose and citrate, metabolites that indicate transition to lactogenesis II, in colostrum samples of women with GDM compared to non-diabetic women. Furthermore, a higher proportion of women with GDM reported a perceived delay in their milk “coming in.” Conclusions: Lower levels of lactose and citrate in the colostrum samples of women with GDM compared to those without GDM indicate delayed lactogenesis II with GDM which may suggest a biological mechanism associated with lower breastfeeding rates among women with GDM. Additionally, maternal perception of delayed lactogenesis II among women with GDM appears to be validated by biomarkers. The implications for practice relate to lactation support in the early postpartum period among women with GDM.