In order to compare the effects of different growth matrices on secondary metabolite production we compared 16 Penicillium species known to produce several families of bioactive compounds. The isolates were grown in rich complex media formulated as semisolid (agar), liquid (still), shake culture, and absorbed in Lightweight Expanded Clay Aggregates (LECA). Both the number of metabolites and their quantities were compared via a chemo-diversity index. The matrix had a profound effect on fungal growth and secondary metabolism in some of the investigated species. LECA was shown to be a powerful alternative for production of sporulation-associated metabolites, such as cyclopenins and viridicatins, for quick up-scaling from agar based media, and as an alternative for production of metabolites that are not induced under submerse conditions.