Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) could be considered as two major techniques of detecting the secondary metabolites produced by microorganisms. Common MS-based analyses such as (GC-MS), (CE-MS), and (LC-MS) are high-throughput methods that provide broad coverage of many classes of secondary metabolites, including amino acids, lipids, sugars, and organic acids etc. Depending on the metabolites you want to analyze, the HPLC also can be used by selecting the correct column and the detector for the analysis of specific metabolites.
I agree with Sandhya Jayasekara about the NMR and MS techniques to characterize the chemicals in your sample, though the data will be much easier to interpret if you separate the compounds first. Any kind of chromatography will be useful, but HPLC will allow you to easily collect samples of each of your secondary metabolites.