That all three goals came from set pieces - two from headers by defenders that would have been easily prevented with the simple provision of a man on each post shows the danger of Mark Hughes trying to change too much too soon.
It was all very annoying for a sizeable travelling support, because Stoke were well in the game when Geoff Cameron equalised in the first half and could easily have extracted a point from a game with the league's form team had they done the defensive basics better. This would never have happened in Pulis' day.
Seven wins on the spin now for the league-leading Gunners.
Full Time - Arsenal 3 Stoke City 1
90 + 3 min Palace 0 Swansea 2 is the final score in the other early game.
90 + 2 min Giroud is growing rather weary of the physical approach of Shawcross and Huth and he's taken another whack for his troubles here. Arsenal get the ball moving again and Ramsey turns into the area before drawing a save from Begovic with a powerful shot.
90 min Arsenal rolling the ball backwards and forwards happy to see out normal time, and four minutes that are being added to the end of the game. Some Arsenal fans are cheering every pass but most are, as is the tradition at this stadium, making an early escape.
86 min Not a lot of belief about Stoke now, which is understandable given the score and the time, but Walters wins a cross in the area and Ireland volleys over as they try and threaten a second goal. Dean had penalised Walters for pushing in any case.
82 min Pennant swings over a corner that's cleared out to the edge of the area where Arnautovic, in a bit of an odd place for a lone striker, mishits a first time volley that's blocked away.
80 min Mesut Özil goes off to a standing ovation from the Arsenal fans.
79 min Shawcross has a volley of abuse for the assistant referee about some perceived holding he felt he was victim of at the last corner. Mike Dean calls him across for a quick word, possibly on a theme of 'pot, kettle, black'.
76 min Two near misses from Ryan Shawcross in a minute. Both chances come from corners, the first he hooks over via a deflection, the second he heads wide from six yards out under pressure.
74 min Stoke substitute Kenwyne Jones and bring on Jermaine Pennant. The former Arsenal man is going to play wide left, presumably with the idea that he can cut in onto his right and offer support to the new lone striker in the system Arnautovic. Arsenal take off Serge Gnabry, who can be very pleased with his afternoon's work, and send on Ryo Miyaichi who is only on the bench today because of Walcott's late withdrawal. Monreal has come on for Jack Wilshere as well.
73 min So Stoke have conceded three goals from set pieces today, including two headers from defenders. Özil put the ball in for all three and two of them would have been cleared easily had Stoke placed a defender on the back post. Somewhere out there Tony Pulis has taken himself for a walk to the end of the garden shaking his head.
GOAL! ARSENAL 3 Stoke City 1 (Bacary Sagna 71 min)
Stoke's tactic of fouling any Arsenal player who gets into full flight in the attacking third continues as Walters bundles over Wilshere. Özil takes the free kick, Sagna climbs at the far post and sends a looping header over Begovic and, several minutes later, into the far corner of the net.
68 min Same again. Stoke attack down the right, Walters crosses low this time, Flamini stabs it behind. The corner is cleared but the amber warning light is on for the home team.
67 min Attractive, eye catching move down the right between Ireland and Nzonzi finishes with a low cross that Szczesny claims before Jon Walters can equalise.
65 min Stop me if you've heard this one before: Jack Wilshere has picked up a knock and requires treatment. It's a chance for a round of drinks for everybody else at the midway point of the half, and for Stoke to send on midfielder Wilson Palacios instead of left back Eric Pieters - Marc Wilson will almost certainly drop back into Pieters' role.
63 min Stoke go straight to the other end of the field and Szczesny beats a shot from Marc Wilson out for a corner.
62 min New Stoke get caught out by a long ball down the middle of the field from Szczesny. Huth allows it to drop in behind him and Wilshere feeds Özil who hits a low shot that Begovic saves comfortably.
58 min Stoke take off Charlie Adam and bring on Stephen Ireland. Adam looks grumpy about it.
57 min That period of concerted Arsenal pressure actually sparks the home crowd into a chant of "We love you Arsenal". I wondered what it was at first, given that the only noise to this point has been the persistent booing of Ryan Shawcross. It's had all the atmosphere of a Richard Clayderman concert so far.
56 min Özil feeds Giroud in the right channel but his attempt to curl the ball around Begovic is badly miscued and flies away to safety.
55 min Huth might want to watch his step here. Now he's busy planting an arm in the back of Giroud's neck and smashing him to the ground. Özil's free kick is cleared.
52 min Stoke almost master their own downfall. Adam turns on the halfway line and plays a blind pass straight to Ganbry. Huth comes across to deal with the situation in his own special way: swatting the puny boy aside like The Simpson's Rainier Wolfcastle in full on McBain mode. Mike Dean waves advantage as Giroud is through and Begovic produces a camera save to turn aside his 20 yard shot. No surprise that Dean goes back and books Huth as Gnabry sets about picking his teeth out of the grass.
49 min News reaching us from Selhurst Park that it's now Crystal Palace 0 Swansea City 2 with a goal from Nathan Dyer immediately after half time. The Swans have been to Valencia and South London in four days and with 40 minutes left for play are currently 5-0 up on aggregate.
48 min Gnabry is certainly a confident boy. He moves inside from the right, checking onto his left foot, which Stoke probably think is a bit of a result after the pasting he's given them down the wing so far, but they're fortunate his cleanly struck left footed shot flies straight to Begovic.
47 min Mark Hughes already unimpressed with what he's seeing. He's sitting down, alone, on the front row of the dugout, waving his right arm in the air and ranting about something. He looks like that old man that every village has who wonders up and down the high street and shouts at the parked cars.
45 min No changes to either side at half time. A reminder that Theo Walcott pulled out during the warm up and was replaced by Serge Gnapry who has been excellent wide on the Arsenal right on his full league debut.
14.35 Second half begins.... Now.
14.25 Half time scores from elsewhere and then a few birthdays... Crystal Palace 0 Swansea City 1 (Michu 2 mins). If you're into league tables after four and a half games, then Arsenal are currently two points clear at the top. Swansea climb seven to tenth.
Time to rummage through the postbag and see what you've had to say for yourselves on today's question of whether Arsenal made the best signing of the summer by bringing in Mesut Özil. William Hargreaves has been in touch to go one further and say it's not only the best signing of this summer, but potentially the best of the modern era. He says: "Özil the best signing by a distance. I think that we will look back in five years time as him being the best Premier League player of the period."
45 + 3 min No further incidents, so it's time for oranges and motivational speeches.
45 min We'll have three extra minutes, then lunch.
44 min He'll have to wait a little bit longer though, because Jones and Mertesacker have clashed heads and both require treatment. Nasty head injuries becoming a bit of a theme for the season at the moment - Romelu Lukaku didn't even know he'd scored Everton's winner at West Ham yesterday after taking a whack in the chops. I give it one more incident before the idea of players wearing helmets is raised.
42 min Pieters wrestles with Gnabry down by the corner flag, taking liberal chunks of Arsenal shirt and and shin bone. It's a soft free kick to give away but Stoke clear with few problems this time. Mark Hughes almost certainly take half time now if offered.
40 min Özil's seizes on Begovic's poor clearance, races down the right flank and cuts the ball back to Gnabry who shoots over. Not Begovic's finest half of football this.
38 min We're now back where we were 20 minutes ago. Stoke requiring a foothold in the game, Arsenal looking like the might cut loose. Wilshere feeds in Giroud but Begovic races from his line to claim the ball first.
36 min This transformation from 'Tony Pulis' Stoke City' into 'Mark Hughes' Stoke-elona' has a number of drawbacks. Not only have Stoke not threatened from their own set pieces, or bothered with their trademark long throws, but they've looked vulnerable defending a dead ball at the other end.
GOAL! ARSENAL 2 Stoke City 1 (Per Mertesacker 35 min)
Just as he did a few minutes before Mertesacker meets a corner at the near post and the ball drops into the far bottom corner with Begovic distracted by Koscileny rushing in unmarked trying to get a touch. It's the German's goal though.
31 min Wilshere is starting to have real influence on this match now. He's on the end of a flowing move in the Stoke penalty box but the shot is deflected away for a corner. Mertesacker meets Özil's delivery and it looks goalbound but Stoke clear from the line.
29 min Wilshere almost, almost has Giroud through on goal but Huth and Shawcross close out the situation.
27 min Totally different game all of a sudden. Gibbs' loose touch gives Jones a clear sight of the Arsenal goal but his control is equally poor and Mertesacker mops up. Credit to Stoke for fighting their way back into a game that only looked to be going one way in the first quarter of an hour.
GOAL! Arsenal 1 STOKE CITY 1 (Geoff Cameron 25 min)
Problem solved. Deep cross to the back post is volleyed skillfully against the post by Arnautovic and Cameron sweeps home the rebound from the edge of the box with Szczesny committed to the first effort.
24 min Left back Kieran Gibbs cuts in from the left wing but lashes a shot high over the bar and off towards Camden Town.
22 min Perhaps a set piece holds the key... A free kick won right on the cusp of the Premier League by Adam is cleared by the wall initially, and then behind for a corner by Koscielny and Arsenal; clear their lines.
21 min So Stoke have a bit of a problem here. They've only scored three goals in four league games so far and been kept scoreless twice already this season. Lone striker Kenwyne Jones hasn't scored a league goal in 2013. Falling behind early was a worst case scenario for them and allows Arsenal to calmly keep the ball and await further opportunities.
16 min This is a Stoke side with no long thrower. One by the corner flag is played short and wasted. Those adverse to change will be wholly uncomfortable watching this. Szczesny in the Arsenal goal must be delighted.
13 min Arsenal force their first corner of the game. Again the Gunners raid down the right with Gnabry but the delivery from Özil is easily claimed by Begovic, which might help his mood after that first goal.
11 min Mark Hughes' touch isn't what it was. A clearance flies out of play towards him in the technical area and he attempts to return it with an elaborate volleyed back heel that sends it skewing off down the touchline. Hughes is playing it cool, hands in pockets, but he'll be furious with that one.
9 min Quick update on Theo Walcott who was named in the starting 11 but pulled out in the warm up. Walcott was ill yesterday, and suffered an abdominal injury prior to this game and has been replaced on the bench by Ryo Miyaichi. Wilshere is limping around now, so the injury worries could be about to get worse...
7 min Stoke need to get a foothold in this game quickly. Arsenal are in flying form, particularly down the right flank with Gnabry impressing on his first start. Another move ends with Cameron upending Wilshere on the edge of the box but it's a fair tackle this time and play is waved on.
GOAL! ARSENAL 1 Stoke City 0 (Aaron Ramsey 4 min)
Not 0-0 today. Pattern being set early here as Arsenal try and cut through with the ball at Wilshere's feet and Charlie Adam bundles him to the ground. This free kick is closer to goal and Özil tries his luck with a left footed shot around the wall. Begovic gets down comfortably to the ball but parries it back into the danger zone and the man of the moment Aaron Ramsey is on hand to tap in from close range. Begovic will be very disappointed with his part in that.
2 min Huth is penalised for an early handball midway into his own half of the field but Arsenal are still in full-on give-everybody-a-feel-of-the-ball mode and elect against putting the ball into the box, where they're at a clear physical disadvantage, in favour of trying to pick a way through the massed Stoke ranks. Comes to nothing.
13.30 We're underway in North London. Stoke, in a lively black and fluorescent yellow number, kicking with their travelling support behind them in the first half.
13.27 Finally ready to go, teams lead out by our referee this afternoon Mike Dean.
13.25 Teams in the tunnel. Well, Stoke are, Arsenal are keeping the visitors waiting. Fair warning, everything I touch at the moment turns into a 0-0 draw. Brace, brace...
13.15 BREAKING TEAM NEWS
Just as Arsene Wenger finishes giving an interview talking about naming the same team and not having injuries, Theo Walcott withdraws at the eleventh hour with illness. Serge Gnabry is moved into the starting 11 for his first Premier League start.
Arsene Wenger on his decision to name Nicklas Bendtner among his substitutes: "He has worked very hard and deserves a place on the bench today. Arteta is just back, he's had two days training and is a bit short but it's good to have him back if needed."
Stoke manager Mark Hughes on Arnautovic's promotion into his starting 11: "He's an exciting talent. We're all curious about how he deals with the Premier League, it's about exposing him to it and seeing how he gets on. He'll be a big talent for us and affect the game in a positive manner. I think he'll lap it up."
12.55 Those of you missing Mario Balotelli's unique brand of behaviour and self control since his departure from Man City could do a lot worse than keeping a regular check on Arnautovic's antics over the coming months. Time with Twente in Holland, Inter Milan and Werder Bremen were peppered with the standard disputes with management that every problem child should have on their CV, but plenty else besides.
The man Jose Mourinho said had the "attitude of a child" has previously torn knee ligaments while playing with his dog, told an Austrian police officer he earned so much money he could "buy your life" after being stopped for speeding and fought with numerous team mates at both his clubs and while on international duty. Talent with questionable temperament, just the ticket in what has been a dull start to the top flight season overall.
12.45 Olivier Giroud, four goals in four games in the league this season and another in the Champions League, recovers from knock to knee to lead the Arsenal line.
Stoke drop Matthew Etherington to the bench and give a full debut to Austrian foward Marko Arnautovic.
12.40 Team news for today's game...
Arsenal: Szczesny; Sagna, Mertesacker (c), Koscielny, Gibbs; Flamini, Ramsey; Wilshere, Ozil, Walcott; Giroud
Subs: Viviano, Jenkinson, Vermaelen, Arteta, Monreal, Bendtner, Gnabry
Stoke City: Begovic; Cameron, Shawcross (c), Huth, Pieters; Walters, Wilson, Nzonzi, Adam, Arnautovic; Jones
Subs: Sorensen, Whelan, Pennant, Palacios, Crouch, Etherington, Ireland.
At Ashburton Grove, Stoke put 11 men behind the ball and see if they can play out time without conceding a goal. At the Britannia Stadium it's all bullying, fire and brimstone as they attempt to intimidate points from a physically inferior side. With Tony Pulis in one dugout and Arsene Wenger in the other nothing looked like changing any time soon.
But this, we're told, is a new Stoke. Mark Hughes, wounded by a catastrophic reign as Queens Park Rangers manager and with as point to prove, is busy ripping up the blueprint that has won Stoke a consolidated Premier League place but few friends and is trying to turn them into a more palatable outfit to watch.
Given just how badly Hughes did at Loftus Road, signing a host of big name stars and making grand, outlandish statements about the club's ambition before crashing and burning on the field, Stoke's decision to appoint him as Pulis' successor was a bold one. And as Stoke have used their midfield as little more than ballast for sometime now, four extra dogs to guard the scrap yard, the changes he's trying to make won't be an overnight job.
But things are looking good. Three wins, a draw and a very narrow defeat at Liverpool on day one that would have also been drawn but for a late Jon Walters penalty miss. Man City were second best to Hughes' side last week at the Britannia, and they've already won an away game at West Ham Stoke won just two on the road in the whole of last season, and Hughes didn't manage a single away win in the league during his entire 11 month reign at QPR.
A month ago they'd probably have fancied their chances of causing an upset at Arsenal. The natives were restless when a summer of failed transfer bids, while bitter rivals Tottenham were signing the world and his wife, opened up into a 3-1 home defeat by Aston Villa on day one.
But in Mesut Özil the Gunners have made arguably the Premier League signing of the summer, and in Aaron Ramsey they have a player reborn and finally starting to fulfil the potential before he fell victim to an appalling tackle and shattered shin at the hands of Stoke's Ryan Shawcross three years ago. Özil's home debut and Ramsey v Shawcross interesting subplots to this lunch time game.
Ramsey shows the value of working with and coaching as player you already own, rather than immediately rushing off to the transfer market at every given opportunity something Spurs might want to consider themselves as each new arrival moves the talented Lewis Holtby further down their pecking order.
Wenger can afford a smug smile after recovering from the Villa debacle to win six on the spin. Despite Stoke's improvement, they're heavy favourites to make it seven today.
Kick-off: 15.00 BST.
TV: Live Sky Sports 1, Highlights BBC ONE Match of the Day2.
Arsenal (Possible, 4-2-3-1): Szczesny; Sagna, Mertesacker, Koscielny, Gibbs; Ramsey, Flamini; Walcott, Özil, Wilshere; Giroud.
Out: Rosicky (thigh), Sanogo (back), Podolski (hamstring), Oxlade-Chamberlain, Diaby (both knee).
Test: Arteta (thigh)
Stoke (Possible, 4-5-1): Begovic; Cameron, Huth, Shawcross, Pieters; Walters, N'Zonzi, Wilson, Adam, Etherington; Jones.Out: Muniesa (groin).
Test: Adam (leg).
Referee: Mike Dean. Matches: 2. R0 Y12.
After winning for a tenth successive game away from home, in Marseille on Wednesday, Arsenal return to the Emirates amd Midfielder Mikel Arteta could return to the squad for the first time this season after a thigh injury.
Santi Cazorla remains sidelined, so record signing Mesut Özil is set for his home debut following his club-record £42 million arrival from Real Madrid.
Czech playmaker Tomas Rosicky is also still out, along with France Under-21 forward Yaya Sanogo, German forward Lukas Podolski and longer-term absentees Alex Oxlade-Chamberlain and Abou Diaby.
Midfielder Charlie Adam has been Stoke's only injury concern ahead of Sunday's game.
The Scotland international needed stitches in a cut after a training ground incident but the Potters expect him to be fit to feature at the Emirates Stadium.
Midfielder Stephen Ireland and forward Mark Arnautovic, who made their debuts off the bench against Manchester City last week, are pushing for first starts.
Aaron Ramsey's trigger-happy start to the season may have grabbed headlines, but it is Mesut Özil who may prove Arsenal's key midfielder here on his home debut.
Mark Hughes has made a quietly impressive start to life at Stoke, who have yet to concede more than once in a game this season.
Özil's rare talent for breaching teak-tough defences will be tested to the full.
Betting: Home 1-3, Away 17-2, Draw 19-5.
Stat of the game: Arsenal have won five out of five home Premier League games against Stoke.
Jonathan Liew's prediction: Arsenal 1 Stoke City 0.