<p>Paratuberculosis is a globally distributed and fatal disease affecting ruminant populations. This study aimed to assess the seroprevalence of paratuberculosis in two large industrial dairy herds of Murciano-Granadina located in Qazvin, and Kerman province, Iran. Serum (<i>N</i> = 1675), and bulk tank milk (<i>N</i> = 2) samples from both herds were analyzed using serum and milk ELISA antibody test, respectively. Several reproductive and productive parameters, including milk yield, services per conception, kidding-to-conception interval, litter size, and gestation length, were compared between seropositive and seronegative goats. The overall apparent seroprevalence differed significantly between two studied herds, which were considered as the control (2.0%, 1/50) and suspected (19.3%, 314/1625) herds (<i>P</i> = 0.002), while the true seroprevalence was estimated at 3.5% and 34.5%, respectively (<i>P</i> &lt; 0.0001). A significant difference in seroprevalence was observed between primiparous does (14.1%) and those with multiple parities (26%) (<i>P</i> &lt; 0.01). Additionally, seropositive goats were significantly older (<i>P</i> = 0.001) and had higher parity (<i>P</i> = 0.003) than seronegative individuals. In terms of production, primiparous seronegative goats produced significantly more milk (<i>P</i> = 0.04) compared to their seropositive counterparts. Seropositive goats also required more services per conception (<i>P</i> = 0.03). The incidence of stillbirths (<i>P</i> = 0.09) and abortions in primiparous seropositive does (<i>P</i> = 0.06) tended to be higher. No other significant differences were observed between the two serogroups. In conclusion, the seroprevalence of paratuberculosis significantly varied. Furthermore, seropositive does, particularly during their first parity exhibited reduced milk production and required more services per conception.</p>