Dear @Sara.Aparicio,
Sen2Cor plugin processes one granule at a time, even when a product with multiple granules is supplied (Sentinel-2 L1C products released before 6th December 2016). I did not try to perform atmospheric correction after granules mosaicing, and I do not know if mosaiced granules can be used as input for the atmospheric correction.
I would suggest to first perform atmospheric correction with sen2cor plugin and second mosaic the results together.
In order to avoid differences along granules borders (due to the parameterization of the Visibility value), and if it may fit your analysis needs, I advice you to set the ‘VIS_Update_Mode’ flag in ‘L2A_GIPP.xml’ configuration file to value ‘0’, as suggested in this post:
Hope to get opinions from other users too!
Federico