Updated flowchart of the calibration method used in J-PLUS DR2. Arrows that originate in small dots indicate that the preceding data product is an input to the subsequent analysis. Datasets are shown with their project logo, and external codes or models are denoted with gray boxes. The rounded boxes show the calibration steps. The asterisks indicate those steps based on dust de-reddened magnitudes. The white boxes show intermediate data products, and ovals highlight data products of the calibration process. The changes with respect to J-PLUS DR1 calibration are the modification in the assumed dust extinction and the addition of the metallicity-dependent stellar locus step in the homogenization (Sect. 3.5).