Secondary metabolites like pyrrolizidine alkaloids (PAs) play a crucial part in plant defense. We studied the effects of soil-borne microorganisms and soil-type on pyrrolizidine alkaloids in roots and shoots of Jacobaea vulgaris. We used clones of two genotypes from a dune area (Meijendel), propagated by tissue culture and grown on two sterilized soils and sterilized soils inoculated with 5% of non-sterilized soil of either of the two soil-types. Soil-borne microorganisms and soil-type affected the composition of PAs. By changing the composition rather than the total concentration below and aboveground, plants have a more complex defense strategy than formerly thought. Interestingly, a stronger negative effect on plant growth was found in sterilized soils inoculated with their ‘own’ microbial community suggesting that pathogenic and/or other plant inhibiting microorganisms were adapted to their ‘own’ soil conditions.