While detrimental effects of reduced plasma progesterone concentration in the early luteal phase on conceptus development in horses have recently been demonstrated, there is no information on associated effects on the endometrium, allantochorion (AC), and chorionic girdle (CG) in this species. We hypothesised that reduced early postovulatory progesterone concentration in pregnant horses is detrimental to endometrial function and development of the embryonic membranes and is an underlying cause of delayed conceptus development. After insemination and ovulation, mares (n = 11) were assigned to treatment (TREAT) or control (CON) during two pregnancies. In TREAT pregnancies, mares received a PGF2α analogue for four consecutive days starting on the day of ovulation with the aim to reduce progesterone secretion. Mares were left untreated in CON pregnancies and thus served as their own controls. Endometrial biopsies for analysis of histomorphology, epidermal growth factor (EGF) and EGF receptor (EGFR) mRNA and protein expression in the endometrium, AC, and CG as well as abundance of regulatory T lymphocytes (Tregs) were collected on day 34 of pregnancy. Histomorphometric analysis revealed a higher luminal endometrium and a higher CG epithelium in CON compared to TREAT pregnancies. Abundance of mRNA for EGF and EGFR was large in the endometrium, AC and CG but did not differ between TREAT and CON pregnancies. The number of endometrial regulatory T lymphocytes was reduced in TREAT compared to CON pregnancies, adding further aspects to the potentially detrimental effects of reduced progesterone concentrations on equine pregnancy.