The design of probiotic hygiene products for daily use is considered an adequate alternative for the restoration of the vaginal microbiome, maintaining health, and/or preventing infections of the female urogenital tract. Most of these probiotic products are available on the world market, but their efficacy and safety are not sufficiently documented. One of the requirements to transfer novel probiotic formulas/products to the productive sector is to demonstrate their innocuity and the absence of adverse or collateral effects on the host, mainly assayed in experimental models. The inclusion of beneficial lactobacilli in nanofibers by electrospinning technique has shown promising application possibilities, and the immobilization of Lacticaseibacillus rhamnosus CRL1332 in nanofibers with and without bioprotective substances and their characterization were previously performed by our research group. In this work, the safety of the intravaginal (i.va.) administration of these functional nanofibers in a murine experimental model was evaluated. L. rhamnosus CRL1332 immobilized in different nanofibers was intravaginally inoculated into mice (seven daily doses). Vaginal washes were taken for microbiological (cultivable lactobacilli) and cytological techniques, and the vagina was used for histological and morphological-ultrastructural evaluation. Our results demonstrated that the intravaginal administration of L. rhamnosus CRL1332 immobilized in nanofibers is safe in murine models, given the absence of an inflammatory response at the cytological and histological levels, with minor modifications at the ultrastructural level, and also related to the normal cultivable vaginal microbiota. On the other hand, the number of cultivable lactobacilli increased in the vagina of mice receiving L. rhamnosus CRL1332 nanofibers. The results indicate the safety of lactobacilli-functional nanofibers and support their inclusion in the design of vaginal probiotic products to prevent/treat urogenital infections and reconstitute the women’s vaginal microbiota.