An anonymous source had told us that there would be a connection between the two, with events taking place in the series that would “tease and set up the S.H.I.E.L.D. of Captain America: The Winter Soldier.”
Well, now series showrunner Jed Whedon is confirming that information with TV Guide, telling them in an interview that the they have plans for the wider Marvel Universe in general and the Captain America sequel in particular.
"We're trying to flesh out the world. The Marvel brand carries with it a lot of familiar faces. We're trying to flesh out the world of S.H.I.E.L.D. with the established characters and the characters we're introducing to build out the larger organization that we operate in," Whedon told TV Guide. Of The Winter Soldier specifically, he added, "Nick Fury [Samuel L. Jackson] is in that one, and S.H.I.E.L.D. makes an appearance, so we will definitely try to tee-up some stuff and probably play a little bit of the fallout from that film. We're hoping to do some cool stuff."
Of course, S.H.I.E.L.D. makes more than just an appearance in the film. It seems to be central to the plot, with Scarlett Johansson having said during Comic Con that the film was basically a S.H.I.E.L.D. movie as much as a Captain America one.