Bacteria producing secondary metabolites with antagonistic effects on fungal pathogens have received attention during the last decades as an alternative to chemical pesticides. They, however, might also have effects on indigenous soil organisms like bacteria and protozoa, the latter ones being among the most important grazers of bacteria in soil. The present study reports on the effect of the potential biocontrol agent Pseudomonas fluorescens CHA0 and its genetically modified derivative CHA0/pME3424 on indigenous soil bacteria and protozoa in a soil system. CHA0/pME3424 overproduces two of the secondary metabolites produced by CHA0: the polyketide antibiotics pyoluteorin (Plt) and 2,4-diacetylphloroglucinol (DAPG). P. fluorescens CHA0/gfp1 and CHA0/pME3424 both negatively affected the abundance of soil bacteria and protozoa and the genetic community structure of Kinetoplastida studied by PCR-DGGE. The negative effects were detectable after 14 days but were decreasing and are expected to be temporary. The overproducer of secondary metabolites did not differ in effect from the wild type. The soil respiration and bacterial genetic community structure were not significantly affected. The study shows the soil bacteria and protozoa to be temporary affected by bacteria producing secondary metabolites, which can have implications for nutrient-cycling in soil and environmental risks of biocontrol agents.