Just as the Captain America film allowed S.H.I.E.L.D. to go in a new direction, the series Agent Carter will create new opportunities for both shows. Said executive producer Jeph Loeb, "We have a unique opportunity in that we have a second series (Agent Carter), and that series is about the origins of S.H.I.E.L.D. While Director Coulson has been given the directive, 'Rebuild this. Make the dream come alive again,' we're also going to go back in time in the other show (to 1946), see the origin of that dream, and where it came from in the first place."
Source: Twitter user Agents of SHIELD