Sonny Perkins opened the scoring for the London side with only two minutes played, and it proved to be enough as Brian Barry-Murphy's side struggled to make an impact in the capital.
City went into the game against second-placed West Ham looking to bounce back to winning ways, but got off to the worst possible start.
Hammers striker Perkins opened the scoring with only two minutes played, latching onto an assist from Kamari Simon-Swyer, handing the home side the lead.
That would prove to be the only chance of the first half, as Barry-Murphy's side struggled to break the hosts down, although we were also able to shut out the hosts following the opener to keep us within touching distance.
Into the second half, the chances started to come, but mostly for the home side as a strong defensive showing from the Hammers restricted the EDS to just two off-target attempts.
West Ham's slender lead ultimately proved to be enough, and saw them rise to the top of the table.
HOW WE LINED UP
Luke Bolton and Kayky took up the winger spots with Oscar Bobb named upfront.
WHAT IT MEANS
The defeat sees us stay in third in the Premier League 2, four points off league leaders West Ham.
It continues a current tough run of form for the EDS, who now haven't won in our last four Premier League 2 encounters.
Next up is a key UEFA Youth League clash against Paris Saint-Germain, taking place at the Academy Stadium prior to the first team clash later that evening. Kick-off is at 3pm (UK).
We will next see the EDS in league action on Monday, 29 November when we take on Leeds United at the Academy Stadium, kick-off is at 7pm (UK).