Elaeagnus moorcroftii Wall. ex Schlecht (EWS) was identified as a suitable food substrate for enhancing the proliferation of Lacticaseibacillus paracasei YL-29 (L.cp29). Metabolomics and pathway analyses were employed to explore the effects of L.cp29 on EWS juice (EWSJ) secondary metabolites and reciprocally, EWS effects on L.cp29 bioactivity and fermentation metabolites. Results indicated robust growth of L.cp29 (9.87 Log CFU/mL) associated with 59 significantly altered metabolites, encompassing 6 classes metabolites. Following fermentation, the downregulation of metabolites, coupled with the upregulation of metabolites, facilitated the accumulation of markers correlated with L.cp29 growth through growth regulating metabolic pathways. Moreover, significant enhancement in the antioxidant capacity of L.cp29 fermented EWS was linked to 127 significantly altered metabolites, including 6 classes metabolites. Downregulated metabolites of EWS were bio-transformed by Lactobacillus, yielding products with higher antioxidant and biological activities compared to their metabolic precursors. Overall, EWS, functioning as a prebiotic, supported L.cp29 proliferation, while L.cp29 biotransformed EWS bioactive compounds into structurally enhanced bioactive forms. These findings underscore a mutually beneficial relationship between EWS and L.cp29, offering insights into the mechanisms governing probiotic and plant-based matrix interactions in functional probiotic fermented foods and suggesting avenues for developing potential synbiotics and postbiotics from Lactobacillus-fermented plant substrates.