<p>Mulberry (<i>Morus alba</i> L.) serves as a high-value woody protein feed resource to address the shortage of protein feed supplies, but inherent limitations, including excessive moisture, insufficient indigenous lactic acid bacteria, and intense protein degradation, constrain its silage preparation. To address these problems, this study developed pre-fermented juices using alternative raw materials, including grape pomace and red clover, which are rich in natural antioxidants, such as polyphenols and isoflavonoids. Four groups were set in the experiment: red clover pre-fermented juice (treatment R), grape pomace pre-fermented juice (treatment G), mulberry pre-fermented juice (treatment M), and blank control (CK). Combined with bacterial community and metabolomic analyses, the present research further investigated their effects on the fermentation quality of mulberry silage during a 60-day ensiling period. The results indicated that treatment R exhibited the optimal comprehensive effect, enriching Enterococcus, upregulating the accumulation of isoflavonoids (formononetin, glycitein, and biochanin A), reducing silage pH to 3.99, elevating lactic acid concentration, and restraining protein degradation by inhibiting protease activity. Treatment M facilitated the proliferation of <i>Lactobacillus</i> and the accumulation of beneficial metabolites such as 3,4-dihydroxybenzaldehyde, while treatment G exerted only a mild regulatory effect. Overall, all pre-fermented juice additions effectively improved fermentation performance and nutrient preservation of mulberry silage. This finding elucidates the mechanism of microbial-metabolite interactions during mulberry ensiling, offers a low-cost, environmentally friendly technical strategy for high-quality silage production, and facilitates the sustainable application of mulberry resources in ruminant feeding systems.</p> Graphical abstract <p></p>