Krystian Bielek rifled home an early opener for the visitors, before Chuba Akpom doubled the Gunners lead before the 15-minute mark.
Stephy Mavididi then added a third for the visitors on the stroke of half time before defender Carl Jenkinson made it 4-0 with 25 minutes remaining.
Striker Macauley Bonne was on hand to continue his fine pre-season form and pull a goal back for the O’s on the 70th minute, but Arsenal added a fifth in the closing stages as Eddie Nketiah smashed home.
On the back of Saturday’s 2-1 victory at Billericay Town, Head Coach Steve Davis made several changes for the O’s final pre-season fixture. David Mooney continued to captain the side in the absence of Charlie Lee, while new signing James Dayton started on the left of midfield.
The fixture was the first time this summer fans had the opportunity to see the O’s in action in E10, but it was the visitors who made the early breakthrough.
Chuba Akpom was superbly denied by Charlie Grainger in the opening seconds, though with three minutes on the clock defender Krystian Bielek smashed home an unstoppable strike from six-yards after Orient had failed to clear from a corner.
Akpom was causing a threat in the Arsenal attack and soon after had a chance to score himself when he latched onto a pass inside the O’s half before seeing his shot parried by Grainger.
The O’s announced the signing of James Dayton shortly before kick-off, and the midfielder had a chance to level the tie on the 12th minute when a cross from the right dropped into his path on the edge of the area. Despite controlling well, Dayton found himself quickly crowded out as his shot came back off Mathieu Debuchy.
Two minutes later Arsenal then doubled their advantage with a neat move, as Chuba Akpom found the back of the net after receiving a clipped pass into the box.
The Gunners were enjoying the majority of possession as a number of crosses flashed across the face of the O’s goal, but as the half progressed Orient grew slightly into the tie with midfielder Rian McLean heading wide from a Josh Koroma corner.
With the interval looming O’s skipper Mooney had a chance to pull a goal back for the hosts when he received a knock-down from Tristan Abrahams following Koroma’s cross, though the forward could only curl his effort wide of the post.
Mooney’s opportunity was not to be the final action of the half however, as Stephy Mavididi added a third for Arsenal on the stroke of half time with a powerful left-footed strike into the top corner.
The O’s fielded a completely different side for the second half as midfielder Alex Lawless took the armband.
Macauley Bonne was another to be introduced into the mix, and the forward found himself inches away from pulling a goal back on the 55th minute as he curled a shot just wide after collecting a pass from Romuald Boco.
Arsenal register their fourth of the night ten minutes later however as Cohen Bramall got forward down the left and pulled the ball back across goal for fellow defender Carl Jenkinson to convert from close range.
Jenkinson then looked to find his second with a powerful strike from outside the area, but his shot was well held by Sam Sargeant with Debuchy ready to pounce.
The O’s were looking to pull a goal back and nearly achieved that when Craig Clay let fly from distance, but his shot was pushed over the bar by Matt Macey.
With 20 minutes remaining there was to be some celebration for the Orient supporters however, as Jobi McAnuff’s low cross from the right was converted by Bonne for his fifth of pre-season.
The goal appeared to liven the hosts up even more, and Bonne followed up by directing a header just over the crossbar before Clay took aim once again from distance with his effort also failing to hit the target.
Despite the O’s best efforts to find a second, it was Arsenal who managed to force another goal as forward Eddie Nketiah smashed home at the third time of asking after Sargeant had brilliantly denied the visitors twice.
With only three minutes of normal time remaining the O’s had a wonderful opportunity to claim a second as Boco picked out McAnuff in acres of space with a wonderful clipped pass, but the midfielder could only head over.
McAnuff’s late opportunity proved to be the final piece of action of the night, as the O’s wrapped up their pre-season campaign ahead of Saturday’s trip to Sutton United for the opening day of the 2017-18 Vanarama National League season.
ORIENT FIRST HALF XI: Grainger, Caprice, Coulson, Elokobi, Widdowson, McLean, Ochieng, Koroma, Dayton, Mooney (C), Abrahams
ORIENT SECOND HALF XI: Sargeant, Judd, Sendles-White, Clark, Happe, Lawless (C), Clay, Moncur, Boco, McAnuff, Bonne
SUBS: Pollock, Barker, Alderson
GOALS: Bonne (70)
ARSENAL U23s: Macey, Jenkinson, Bielek (Johnson HT), Debuchy, Pleguezeulo (C), Bramall (Mourgos 70), Reine-Adelaide (McGuane 70), Toral, Mavididi, Nketiah, Akpom (Malen 34)
GOALS: Bielek (3), Akpom (14), Mavididi (45), Jenkinson (65), Nketiah (79)
ATTENDANCE: 2,006 (140)
REFEREE: Darren Deadman