Vitamin C (VC), or ascorbic acid, is vital for various physiological processes, including oxidative stress prevention, collagen synthesis and brain development and function. Most mammals synthesize VC through an evolutionarily conserved pathway where GULO performs the last step of the synthesis. Nevertheless, within bats, a complex evolutionary history with multiple independent GULO gene losses has been reported based on a limited sample of 16 bat species from five families. Currently, 167 bat genomes representing 93 species (13 families) are available at the NCBI genome database. Nevertheless, only 33 genomes have been annotated. The lack of a genome annotation for most species prevents the use of the available data, as well as the inference of a reference phylogeny for bats, needed to contextualize the GULO findings. To overcome these issues, a SEDA-Compi gene-evolution pipeline was developed to explore GULO evolution in bats using all available genome data. Nevertheless, the pipeline can also be used to study other genes and taxonomic groups, since a large fraction of genomes is non-annotated in most of them. Our analyses support three GULO losses in bats, namely, one at the base of the Yangochiroptera lineage, about 65 Mya, and two independent losses within the Pteropodidae family, in the lineage leading to Pteropus and Cynopterus (for both about 55 Mya).