Fermented foods have a long history of human use. The purpose of this study was to characterize the microbial composition of a traditional fermented wheat preparation—Nishasta— and to explore its effect in retinoic acid-induced osteoporosis in Wistar rats. The sample was suspended in sterile water (10% w/v), mixed thoroughly, filtered, and gradually diluted. Aliquots of dilutions were cultured in MRS (DeMan–Rogosa–Sharpe) medium, and colonies with similar morphologies were subjected to DNA extraction. The 16S rRNA gene of the isolates was amplified by polymerase chain reaction, checked by agarose gel electrophoresis, and finally identified by sequencing. Anti-osteoporosis screening of Nishasta was carried out in female Wistar rats using retinoic acid as an inducer (70 mg/kg, p.o. once a day for 14 days). Its effect on bone health parameters was determined. The bone metabolism markers such as hydroxyproline (HOP), tartrate-resistant acid phosphatase (TRACP), and alkaline phosphatase (ALP) were evaluated. The results of microbial characterization revealed the presence of ten clones of Lactobacillus plantarum in the fermented preparation with L. plantarum NF3 as the predominant strain. The average microbial count was 2.4 × 103 CFU/g. Retinoic acid administration led to a marked disorder of various bone health markers in rats. It also increased the levels of urine calcium and phosphorus, indicating increased bone destruction. Treatment with fermented wheat (at 200, 100, and 50 mg/kg doses, p.o. daily for 42 days after the induction of osteoporosis) improved bone mineral density in a dose-dependent manner. It also improved the bone microstructure and reduced the levels of ALP, TRACP, and HOP. Micro-CT revealed that it reduced trabecular separation and increased the percent bone volume, trabecular numbers, trabecular thickness, and bone mineral density in the rats. The results showed that the fermented wheat promoted bone formation and prevented bone resorption. Our findings clearly established the effectiveness of Nishasta against osteoporosis in Wistar rats that can be partly attributed to the improved gut calcium absorption and microbiota composition.