Our study explores the differential effects of Bothrops moojeni venom and its fractions on osteoclast (OC) morphology, function, and osteoclastogenesis. The crude venom and its high-molecular-weight (HMW) fraction disrupt critical OC processes, including F-actin ring formation and mitochondrial distribution, thereby impairing bone resorption. These components primarily target cytoskeletal integrity and transcription regulation, with the OBSCN gene playing a direct role in OC function. In contrast, the low-molecular-weight (LMW) fraction selectively modulates OCs without significant cytoskeletal alterations. It influences vital cellular signaling pathways, notably through FNIP1 and FNIP2, essential for OC differentiation and function. This suggests a more targeted therapeutic approach with potentially fewer off-target effects. The venom also alters cytokine production, increasing IL-6 and IL-10 levels. Elevated IL-6 levels promote osteoclastogenesis and bone resorption, while IL-10 appears to counterbalance these effects through a regulatory feedback mechanism. Secretome analysis reveals that the crude venom and HMW fraction disrupt proteins involved in membrane trafficking and structural integrity. In contrast, the LMW fraction influences matrix remodeling, energy metabolism, and gene regulation. Gene interaction analysis LMW fraction post-treatment identifies FNIP1 and FNIP2 as critical targets involved in osteoclastogenesis. The observed changes in gene expression, including those related to immune response, energy metabolism, and chromatin remodeling, provide insights into the venom's impact on bone health. Overall, the LMW fraction shows promise for drug development due to its selective implications and potential for fewer side effects, offering a more precise approach to treating bone diseases.