During ECMO therapy, infections are common and have substantial impact on treatment outcomes. However, data on the prevalence and clinical impact of microbial ECMO cannula colonization are scarce. Between October 2020 and May 2022, we evaluated 112 ECMO cannulas from 58 patients for microbial colonization using sonication fluid culture & 16S-rRNA-PCR (n = 105), or roll plate method (n = 7). 38 (33.9%) cannulas from 30 (51.7%) patients showed evidence for bacterial colonization with the predominance of coagulase-negative staphylococci (67.4%). Antipseudomonal β-Lactam treatment at cannulation and ECMO initiation at referring hospitals were associated with cannula colonization upon multivariable per-patient analysis. The prevalence of bloodstream infections was equally low and the occurrence of fever after and number of anti-infective drugs given during ECMO therapy was similar in patients with and without exposure to colonized cannulas. Finally, there was no association of cannula colonization with adverse outcomes. In summary, our data suggest that bacterial ECMO cannula colonization does not affect the clinical course of patients and thus discourage routine microbial assessment of cannula tips or even cannula exchange in the absence of clinical signs of cannula infection.