Abstract Sex steroid concentrations modulate endometrial function and fertility in cattle. Our objective was to compare the post-estrus luminal transcriptome of cows that were exposed to contrasting concentrations of progesterone (P4) before luteolysis that displayed estrus and ovulated spontaneously. Cross-bred beef cows received either (1) a new CIDR and GnRH (day −9; high progesterone treatment; HP4; n = 16) or (2) a previously used CIDR, PGF2α, and GnRH (low progesterone treatment; LP4; n = 24). All cows received PGF2α at CIDR removal (day −2). Ovarian ultrasonography and blood collections were performed on days −9, −2, −0.5, and 0 (day of observed estrus), and days 4, 7, and 14 for measurement of ovarian structures, P4, and estradiol (E2). Luminal epithelial cells were collected using a cytology brush on days 4, 7, and 14 for RNAseq. On day −2, CL area and concentrations of P4 were greater, while on day −0.5, concentrations of E2 were decreased in HP4. Ovarian structures and hormonal concentrations were similar on days 4, 7, or 14 (P > 0.05). There were enriched pathways in HP4 related to activation and signaling of the innate immune system at day 4, downregulation in the network involved in the extracellular matrix remodeling at day 7, and exacerbated inflammatory response as well as differentiation and activation of macrophages at day 14 (Benjamini–Hochberg P-value ≤ 0.05). In conclusion, manipulation of pre-luteolysis sex steroid concentrations altered the post-estrus luminal transcriptome even though all cows showed estrus and ovulated spontaneously.