A Paul Mullin’s second half effort from range was the only goal of the match that sealed all three points for the visitors and extend their unbeaten run to five games now.
Danny Webb made two changes to his sides that lost 2-1 at home to high-flying Carlisle at the weekend, as Yvan Erichot replaces Callum Kennedy and Victor Adeboyjo got the nod for his first league start ahead of new signing Rowan Liburd.
Gavin Massey got the crowd off their feet early with an opperutnity four minutes in, as his low cross found Nigel Atangana but he could not make the right connection as it trickled through to Barry Roche.
Morecombe threatened after Orient’s early pressure, as the ball came to the far post for Kevin Ellisons’ to strike but was headed away by Tom Parkes.
Erichot made a huge crossfield pass to turn defence into attack, which found Sandro Semedo – he burst into the box and hit his low cross which was stopped by Roche and out for a corner.
Orient worked a great chance and were almost rewarded with a goal on the half hour mark, as Collins slotted in Massey whose shot with the outside of his boot was pushed around the post by Roche.
From the resulting corner, the ball fell to Collins inside the box and his snap shot went just the wrong side of the post.
The O’s heaped even more pressure on the Morecombe defence, as Semedo’s corner was met by Parkes at the back post but headed straight into the arms of Roche.
The hosts almost broke the deadlock just before the break, as Massey flashed a low ball acorss the six-yard box just out of the reach of Sam Dalby and Adeboyejo.
In the second half, Orient again were the dominant side and set the pace with Myles Judd advancing on the edge of the area clipped the ball back to Semedo whose shot was tame.
Morecombe so nearly got the opener, as Ellison was played through one-on-one and his shot was superbly stopped by Sam Sargeant to deny the away side the lead.
Orient used the same cobination again form the corner kick, as Semedo’s whipped in ball was headed just over the bar by Parkes.
Morecambe still showed their threat on the counter attack, as Paul Mullin early ball into the box was turned just over the bar by substitute Rhys Turner.
The visitors struck 72 minutes in, as Mullin had the ball on the edge of the area and whipped his shot into the top corner, to stun the O’s.
Orient pushed for the equaliser but struggled to create a clear cut chance, as they remain in the bottom two.
Leyton Orient Lineup: 24 Sam Saregant, 6 Tom Parkes, 7 Michael Collins (89), 11 Gavin Massey, 15 Nigel Atangana, 16 Nicky Hunt (C), 22 Sandro Semedo, 26 Victor Adeboyejo (90), 29 Myles Judd, 30 Sam Dalby (77), 37 Yvan Erichot
Substitutes: 12 Charlie Grainger, 4 Liam Kelly (89), 14 Sammy Moore, 19 Teddy Mezague, 20 Rowan Liburd (77), 28 Josh Koroma (90), 34 Michael Clark
Morecombe Lineup: 1 Barry Roche, 5 Ryan Edwards, 6 Dean Winnard, 7 Paul Mulin (81), 8 Peter Murphy (C), 10 Lee Molyneux (65), 11 Kevin Ellison, 15 Aaron Wildig, 16 Alex Whitmore, 19 Michael Duckworth, 24 Michael Rose (75)
Substitutes: 12 Dan Nizic, 2 Liam Wakefield, 3 Aaron McGowan (81), 4 Alex Kenyon (75), 14 Luke Conlan, 18 Rhys Turner (65), 21 Antony Evans
Attendance: 2,660 (58)