@Oak-tail
For comics there aren’t really clear “seasons” like the show, but a good starting point is the first year’s worth of comics, which all take place chronologically after the season 2 finale but before the season 3 finale. These are:
Issues #1 to #12 of the main book, which are also collected in trades as Volumes 1 to 3.
The 10 issue “Micro-Series” side book (aka Pony Tales Volume 1 & 2).
The special issue called “MLP Annual 2013”, which is a prequel to Equestria Girls.
Now, what is the best reading order? The main book has multi-part stories while the side books are all one-shots. It’s more fun to read story-arcs without interruption, so here is my recommended reading list that preserves original publication order but doesn’t split up story-arcs:
Friendship is Magic #1-4
Micro Series #1-3
Friendship is Magic #5-8
Micro Series #4-6
Friendship is Magic #9-10
Micro Series #7-8
Friendship is Magic #11-12
MLP Annual 2013
Micro Series #9-10