Bees are the most important group of flower visitors providing an essential ecosystem service, namely pollination. Due to the worldwide decline of bees, there should be standardized sampling methods in place to ensure consistent and comparable results between studies. We compared the two commonly used sampling methods of yellow pan traps and transect walk to determine (i) which habitat variables affect the species composition, abundance and species richness of sampled bee communities, (ii) which method potentially contains sampling bias towards some individuals or groups of bees and (iii) the efficiency of sampling in various habitats. We conducted fieldwork in different agricultural habitats distributed along landscape heterogeneity and topography gradients. Our results showed that the height of vegetation, the average number of flowers and the amount of woody vegetation had the greatest influence on the sampling efficiency. Our survey also demonstrated that sampling by transect walk captured less bees in general, especially in stubble, maize, and cereal fields. We found that