<p>This study evaluated the effects of synchronization with Presynch–Ovsynch or Double-Ovsynch protocols on first-service conception rate (FSCR) in cows with and without subclinical endometritis (SCE). We hypothesized that the negative effect of SCE on FSCR would be evident under Presynch–Ovsynch but mitigated under Double-Ovsynch. A total of 314 Holstein cows from four semi-technified Mexican dairy farms were included. Uterine cytology at 30 ± 5 days postpartum was used to diagnose SCE, and pregnancy was confirmed 45 days after insemination. Fisher’s exact test and logistic regression were used to evaluate associations between SCE, synchronization protocol, and FSCR. Among cows synchronized with Double-Ovsynch, FSCR was lower in SCE-positive than SCE-negative cows (29.6% vs. 43.8%, <i>P</i> = 0.040). A similar trend occurred in Presynch–Ovsynch cows (35.0% vs. 47.2%, <i>P</i> = 0.059). Logistic regression identified SCE as the only variable trending toward significance (<i>P</i> = 0.086, OR = 1.6; 95% CI: 0.935–2.782), suggesting that SCE increases the risk of reduced FSCR. No significant interaction between synchronization protocol and SCE status was found (<i>P</i> &gt; 0.1), and Double-Ovsynch did not improve FSCR over Presynch–Ovsynch. Among SCE-negative cows, Presynch–Ovsynch tended to yield higher FSCR than Double-Ovsynch (47.2% vs. 43.8%, <i>P</i> = 0.093). In SCE-positive cows, FSCR remained low across protocols with no significant difference (<i>P</i> = 0.160). Synchronization protocol had no significant FSCR effect in primiparous cows (<i>P</i> = 0.139). In multiparous cows, the observed trend suggested a potential Presynch–Ovsynch advantage (<i>P</i> = 0.082). In conclusion, in semi-technified dairy farms, SCE significantly reduces FSCR, regardless of the synchronization protocol, while Double-Ovsynch does not mitigate this effect.</p>