In this section of the page, we will see evidence seen on the official Marvel pages that the 6 series are canon.
MCU Nick Fury Biography: The MCU Nick Fury biography mentions the events that occurred in the final episode of Agents Of S.H.I.E.L.D. Season 1, where Fury helps Agent Phil Coulson defeat John Garrett, a former protégé of Fury who had revealed himself to be The Clairvoyant.
Numbered Realities: In the section from official universe designations on this page, we see that the official designation of the MCU is Earth-199999 / MCU-616, which has been used to refer to branching universes of the latter, such as Frank Castle's dreams seen in The Punisher series, the alternate universes of What If...?, and, the ones that matter most to us here: there are two official designations where they mention that the events of Agents Of S.H.I.E.L.D. take place in the MCU.