The present invention relates to an improved process for isolating aliphatic, mono- or polycyclic small molecules, in particular, Cycloclavine or Cornexistin and/or Hydroxycornexistin, from the aqueous fermentation broth of a eukaryotic microorganism. Said process comprises contacting a liquid phase of said fermentation broth containing said active ingredient with a suitable adsorbent, desorbing said active ingredient from said adsorbent, optionally performing a second chromatographic purification step, and isolating the active ingredient in substantially pure form. The thus obtained purified small molecules may be further used in biocidal, i.p. insecticidal or herbicidal compositions.