Microbial fermentation of plant extracts with Lactobacteria is an option to obtain microbiologically stable preparations, which may be applied in complementary medicine. We investigated the metabolic conversion of constituents from Mercurialis perennis L. extracts, which were prepared for such applications. For this purpose, aqueous extracts were inoculated with two Lactobacteria strains, namely Pediococcus sp. (PP1) and Lactobacillus sp. (LP1). Both were isolated from a fermented M. perennis extract and identified by 16S rRNA sequencing. After 1 day of fermentation, an almost complete conversion of the genuine piperidine-2,6-dione alkaloids hermidine quinone (3) and chrysohermidin (4)—both of them being oxidation products of hermidin (1) —was observed by GC-MS analysis, while novel metabolites such as methylhermidin (6) and methylhermidin quinone (7) were formed. Surprisingly, a novel compound plicatanin B (bis-(3-methoxy-1N-methylmaleimide); 8) was detected after 6 days, obviously being formed by ring contraction of 4. An intermediate of a postulated reaction mechanism, isochrysohermidinic acid (14), could be detected by LC-MS. Furthermore, an increase in contents of the metabolite mequinol (4-methoxyphenol; 9) upon fermentation points to a precursor glycoside of 9, which could be subsequently detected by GC-MS after silylation and identified as methylarbutin (15). 15 is described here for M. perennis for the first time.