The phenomenon of embryonic diapause has been reported to possibly affect ovarian follicular development. The aim of the current study was to identify the impact of the embryonic diapause period on follicle number and oocyte quality in the European roe deer (Capreolus capreolus). In this species, the embryo undergoes five months of developmental delay. We have determined the antral follicle count (AFC), oocyte morphological quality, oocyte meiotic resumption capacity and the transcriptome profile in immature (GV) and in vitro matured (MII) oocytes obtained during embryonic diapause and after embryo reactivation. A drop in AFC, number of oocytes suitable for in vitro maturation and oocytes reaching the MII stage was observed after embryonic reactivation. A large impact of the diapause period was evident when MII oocytes were compared against GV oocytes using an RNA-seq approach. A total of 1028 genes significantly differed between MII and GV oocytes during diapause and 1795 genes after reactivation. These genes included PDE3A and SOD2, known for being involved in oocyte meiotic arrest and oxidative stress. In addition, tumour-related genes included NDRG3, NCSTN and UGDH, which have been associated with cell proliferation, migration and metabolism, were found. Comparing diapause versus reactivation, differential transcript abundance in both GV and MII oocytes was observed (44 and 32 differentially expressed genes, respectively). Our results suggest that the embryonic diapause and reactivation periods modulate follicular dynamics, influencing the oocyte towards lower quality after reactivation. This is may be related to increased apoptosis, abnormal mitochondria function/structure and metabolic dysfunction in the maturing oocyte.