Updated flowchart of the calibration method used in J-PLUS DR3. 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 data or models are denoted with black boxes. The rounded purple boxes show the calibration steps. The asterisk indicates the step based on dust de-reddened magnitudes. The blue boxes show intermediate data products, and green ovals highlight data products of the calibration process. The main change with respect to J-PLUS DR2 calibration is the use of Gaia BP/RP low-resolution spectra in the homogenization (Sect. 3.2).