Season 2 of the Abe Series began on May 31, 2012 with The Abraham Trilogy - Part 2: Abe Paints the Town Red and ended abruptly on June 9, 2013 with Abraham Short - Abraham Short. Season 2 drastically cut down the number of episodes in a season from 50 to just 12. The reason for this was the lack of any more ideas and the idea of a series finale starting to cook.

The original plan was to never return to seasons, as stated in Abraham Short - Abraham Short, but in 2016, with the Year of Abe, Season 4 did, in fact, begin, though still approaching the same end-goal of a series finale.

There are several episodes for Season 2 that were planned, but ended up being scrapped. There were two Halloween specials, Franken-Abe and Dr. Mania and the Heinous Manus. Neither of these were ever finished. Abe Travels Through Time: Old Wounds Reopen was meant to be a sequel to Abe Travels Through Time: Abe and Godfrey Save Time, but it was also scrapped. Abe vs. Machine: The Winter of Reno's Downfall, tying in with ATTT2, also began in Season 2, but it is possible that it will be scrapped as well.