Long-term mark-recapture studies are essential for bat conservation. Over the last decades, millions of bats across Europe and America have been marked with forearm rings for this purpose. Although it is considered a cost-effective method compared to Passive Integrated Transponders (PIT) tags, direct injuries from using forearm rings have been reported since their very first use. Yet, their impact on bats' welfare has not been systematically evaluated and remains a highly controversial issue among the scientific community and policymakers. Here we assess the impact of forearm rings and PIT tags on the health of different bat species. We reviewed 12 years of the existing recapture data of free-ranging bats from NE Spain and evaluated the impact of both marking tools in a captive colony of Carollia perspicillata, by assessing the development of skin lesions and levels of cortisol metabolites in guano (CG) after marking. We report that 55.1 % (435/790) of the recaptured free-ranging bats with forearm rings presented skin lesions. All banded C. perspicillata (n = 22, 100 %) developed skin lesions, whereas none of the PIT-tagged (n = 21) presented lesions. Levels of CG were significantly higher after marking with forearm rings only for one group. Banded C. perspicillata exhibited discomfort-associated behaviours due to forearm rings. Under the “precautionary principle”, we recommend the ban of forearm rings for all bat species until species-specific studies under controlled conditions are performed and approved by a legally constituted ethics committee. Consideration of other long-term marking tools is mandatory to align with global bat conservation strategies.