My chillie seeds have germinated in window sill propagators in individual pellets. When do I transfer them to individual pots?

My understanding is that you only pot seedlings on once the roots are showing. This is in general, but I don't know about chillies in particular. Perhaps someone else may answer this question.

I pot mine on from the seed germination stage when there are 2 /4 proper leaves [dont count the seed leaves]. I use 2-3 " pots first and then move up the sizes as craftnutter says i then pot on when the roots get to the bottom of the pot.

I agree with you Seaburngirl. Keep repotting, with the final pot size being a minimum of 10" diameter.