I used this kit on my old Canon S9000 A3 printer which has dye based inks only and it unclogged the heads very well. I have no experience of cleaning heads where pigment based inks are concerned but I can't think of any reason why the cleaner should not work as effectively with pigment ink. However, as you say the pigment head is printing OK I suggest you leave this one alone and just inject the cleaner through the dye heads only. That way you don't need to worry about any possible compatibility issues with pigment ink. Hope this reply is helpful.