Updated project metadata. Arginine phosphorylation, an emerging protein modification, has been lately described to occur in B. subtilis and Staphylococcus aureus. The kinase responsible for arginine phosphorylation in B. subtilis was shown to be McsB, which counteracts the protein arginine phosphatase YwlE. Here we demonstrate that YwlE drives the progression of spore germination by dephosphorylating arginine phospho-sites of target proteins involved in key cellular processes.