In this study, the effects of the Bt-toxin Cry1Ab and a soybean trypsin inhibitor (SBTI) on intestinal bacterial communities of adult honeybees (Apis mellifera) were investigated. It was hypothesized that changes in intestinal bacterial communities of honeybees may represent a sensitive indicator for altered intestinal physiology. Honeybees were fed in a laboratory set-up with maize pollen from the Bt-transgenic cultivar MON810 or from the non-transgenic near isoline. Purified Cry1Ab (0.0014% w/v) and SBTI (0.1% or 1% w/v) represented supplementary treatments. For comparison, free-flying honeybees from two locations in Switzerland were analysed. PCR-amplification of bacterial 16S rRNA gene fragments and terminal restriction fragment length polymorphism analyses revealed a total of 17 distinct terminal restriction fragments (T-RFs), which were highly consistent between laboratory-reared and free-flying honeybees. The T-RFs were affiliated to Alpha-, Beta-, and Gammaproteobacteria, to Firmicutes, and to Bacteriodetes. Neither Bt-maize pollen nor high concentrations of Cry1Ab significantly affected bacterial communities in honeybee intestines. Only the high concentration of SBTI significantly reduced the number of T-RFs detected in honeybee midguts, a concentration that also increases bee mortality. Therefore, total bacterial community structures may not be a sensitive indicator for providing evidence for the impact of insecticidal proteins on honeybees at sublethal levels.