Ebbsfleet staged a late second-half comeback to condemn Stockport to defeat in their first game under caretaker manager Willie McStay.
Nick Chadwick put the Hatters ahead from the penalty spot after Tom Phipp fouled Tom Elliott in the area.
Calum Willock headed the home side level from Joe Howe's cross with 10 minutes remaining.
Nathaniel Pinney then grabbed the winner, firing a low shot past County goalkeeper Mark Halstead.
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Ebbsfleet boss Liam Daish told BBC Radio Kent:
"We kept asking the questions and clear honest endeavour has got us the win. The lads have been fantastic.
"Nobody can grumble at that, our second half performance was superior and there were two late goals.
"It's six games unbeaten, it's a good haul, two weeks ago I remember how down everyone was but two wins on the spin against sides below us, that's a great couple of weeks in the face of adversity."