Of course there are hundreds of ways. Which culture are you tlaking about and what sort of metabolites?
Anyhow, firstly grow small scale medium, and evaluate metabolite initially via TLC, UV, IR, HPLC (Analytical). Then scale up the cell culture and optimize the culture conditions . Determine at what stage of your culture the required metanbolites are getting produced. Filter the culture & isolate via column chromatography. For further purification reverse phase chromatography & Preparative HPLC shall be required depending on nature of compounds of interest. That's all.