Ecoimmunology of wild animals becomes increasingly important. However, there are methodical limitations, especially when working on small mammals, e.g. small sample volume and acute stress associated with capture, handling and sampling that can influence immune parameters. The plasma bacterial killing assay measures innate humoral immune responses, mainly complement activity. It is a powerful tool with many methodical advantages. To avoid investigation of artefacts in future ecoimmunological studies the influence of acute stress on the bacterial killing activity was assessed. Bats (Nyctalus noctula, n = 9) were repeatedly sampled in three time intervals up to 97 min after capture. Bacterial killing activity against Escherichia coli was measured using a microplate absorbance reader. Bacterial killing activity was not influenced by capture, handling and sampling. Hence, released stress hormones did not affect circulating complement activity. To conclude, the plasma bacterial killing assay is reliable and efficient ecoimmunological tool in wildlife studies even of small mammals.