Background: Endophytes with beneficial effects on hosts are potentially utilized in crop managements. However, the use of living endophytes will risk the possible pathogenicity or other ecological problems. Whereby, it will be great value if functions of certain endophytes on crops could be replaced by elicitors extracted from living endophytes. For addressing this issue, the present work therefore compared the impacts of three endophytic fungal strains and their soluble extracts on grape cells at both the transcriptomic and metabolome scopes. Results: Our results revealed that the exposure to living fungi or fungal extracts triggered responses in terms of both the differentially expressed genes (DEGs) and the differentially regulated metabolites (DRMs) in grape cells, with great fungal strain-specificities. Compared to the living fungi exposed grape cells, less DEGs and DRMs responses were initiated in most of the corresponding fungal extracts treated grape cells. Nevertheless, major proportions of specific DEGs, DRMs, and the subsequently enriched GO function terms and KEGG pathways in living fungi treated grape cells were also detected in those fungal extracts exposed grape cells. Conclusions: The work demonstrated that the specific effects of certain living endophytic fungus on grape cells could be replaced or partially replaced by their fungal extracts, and confirmed an alternative approach to utilize endophytes in agriculture with more eco-safety promises.