Intravaginal progesterone sponges have been widely utilized to synchronize estrus in goats; however, extended use may be accompanied by vaginal microbial imbalance, vaginal discharge abnormalities, and diminished reproductive performance. Intravaginal probiotics have been suggested as an alternative to antibiotics for addressing vaginal dysbiosis, but their effects across varying synchronization durations have not been thoroughly studied in goats. The current study was conducted to assess the effect of intravaginal probiotic use in association with various progesterone sponge durations on vaginal microbiota and reproductive effciency in Black Iraqi goats. Forty-four adult goats (2–5 years) were randomly assigned to four groups (n = 11) for 7 and 14 days of treatment with a progesterone sponge alone or in combination with probiotics. Two strains of Lactobacillus (L. plantarum and L. acidophilus) were used in a lyophilized product (2×109 CFU/sponge). The following were assessed: cultivable vaginal bacteria (total bacteria, Enterobacteriaceae, Lactobacillus), score of vaginal discharge, onset of estrus and duration of estrus, and early pregnancy rate. Larger Enterobacteriaceae and total bacterial counts, and lower Lactobacillus counts, were observed with prolonged retention (14 days) compared to the short-duration protocol (p < 0.05). Probiotic treatment showed significantly higher Lactobacillus counts (2.75 ± 0.69 vs.0.44 ± 0.25 log CFU/mL) (p < 0.001) and significantly lower Enterobacteriaceae and total counts, especially in the long protocol (Enterobacteriaceae 4.37 ± 0.36 vs.5.20 ± 0.44; total 5.26 ± 0.43 vs.6.14 ± 0.44 log CFU/mL), with a significantly earlier on set of estrus (29.82 ± 0.66 vs.33.00 ± 1.18 h), longer duration of estrus (29.91 ± 0.79 vs.24.73 ± 0.84 h), and milder discharge (Fisher’s exact test, p = 0.01 –0.03) than controls. The early pregnancy rate was numerically higher in the probiotic-treated groups but not statistically significant (p > 0.05). Overall, the duration of sponge use was associated with vaginal health and reproductive responses, with short-sponge duration protocols with high-dose Lactobacillus associated with decreased dysbiosis and enhanced vaginal health, suggesting a non-antibiotic strategy that warrants testing in larger studies for it spotential role in conception.