The software maker claims that Google used its dominant position in the search market to restrict the growth of Microsoft services.
It cites a number of practices, including Google limiting the ability of Microsoft Bing to index web content.
Google said it was not surprised by the move and it would happily discuss its business with the European Commission.
In a detailed blog, Microsoft's general counsel, Brad Smith, outlined the company's grievances.
He wrote: "Our filing today focuses on a pattern of actions that Google has taken to entrench its dominance in the markets for online search and search advertising to the detriment of European consumers."
The post goes on to list five different ways in which Google, according to Microsoft, has sought to control the search market.
Those are:
The European Commission launched an investigation into allegations of anti-competitive practices by Google last November, at the behest of several internet companies, including Ciao, a shopping site owned by Microsoft.
It is likely, if the Commission accepts the latest round of complaints from Microsoft, that they would be rolled into the same investigation.
For the Microsoft case to be accepted, the company would have to prove two things - firstly that Google was dominant in a particular market, namely search, and secondly that it had abused that position.
In a statement, Google said it would cooperate with any investigation.
"We're not surprised that Microsoft has done this, since one of their subsidiaries was one of the original complainants. For our part, we continue to discuss the case with the European Commission and we're happy to explain to anyone how our business works," is stated.
Penalties for companies found to have engaged in anti-competitive practices in Europe can be severe.  The EC has the power to impose fines up to 10% of global earnings.
That will likely have a bearing on how the case proceeds, according to Mark Tricker, an antitrust lawyer with the law firm Norton Rose.
He told BBC News: "Once the Commission has formulated its claims then I suspect that Google will enter into a dialogue with them to address those concerns so it does not have to reach a judgement."
Microsoft's position as accuser in an anti-competition case is something of a role reversal.
In the past, the world's leading software company has been the target of similar actions.
A 2003 EC ruling determined that Microsoft had unfairly advantaged its Windows Media Player software over other streaming technologies by embedding it into the Windows operating system.
It was fined Â£381m, followed by a further Â£194m in 2006 for failing to comply with elements of the original ruling.
To date, the largest fine levied by the EC was Â£948m against Intel in 2009.
The microchip maker was found to have offered financial incentives to manufacturers to favour its products over those of its rivals.

Sum: Microsoft is to take an anti-competition complaint against Google to the European Commission.


Financial Fraud Action, a body set up by the financial services industry, said that fraudsters were impersonating major companies to steal money.
They claim they are fixing a slow internet connection, but trick firms into allowing funds to be transferred.
Some claim to be calling as a result of recent high-profile data breaches.
"You should never let someone else have access to your computer remotely, especially if they have contacted you via an unsolicited phone call," said Katy Worobec, director of Financial Fraud Action UK.
"If you are in doubt, then call the organisation back on a number you trust; if they are legitimate they will understand."
While "working" on the internet fault, the fraudster claims the victim is entitled to compensation and asks them to log into their bank account.
The scammers still have access to the computer and will put up a fake screen which makes it appear the money has arrived. Working in the background, they will take money from the victim's bank account.
Financial Fraud Action said that con-artists were preying on concerns over recent data breaches. Hacks have compromised businesses such as Talk Talk, Sony and Carphone Warehouse.

Sum: A spate of scams in which criminals use technology to take over victims' computers has been reported by an anti-fraud group.


Ismaaiyl Brinsley, 28, had a history of violence and mental instability.
Candlelit vigils have been held in New York in memory of officers Wenjian Liu, 32, and Rafael Ramos, 40.
Brinsley shot them as they sat in their patrol car in Brooklyn on Saturday before running into a subway station and shooting himself.
Hours earlier, he had shot and wounded his 29-year-old ex-girlfriend, Shaneka Thompson, at her home in Baltimore, Maryland, police said.
The New York Police Department's Chief of Detectives, Robert Boyce, said that for weeks before the shooting, Brinsley had posted anti-police and anti-government messages on his Instagram account referring to the deaths of Michael Brown and Eric Garner.
Protests erupted across the US last month after grand juries in Missouri and then New York declined to charge the white police officers who killed the two unarmed black men.
Chief Boyce said Brinsley had also shared his feelings of "self-despair and anger at himself and where his life was" in recent posts.
When he arrived in New York on Saturday - hours after shooting Ms Thompson in the stomach - Brinsley threatened on Instagram to kill police officers.
"They Take 1 of Ours... Let's Take 2 of Theirs #ShootThePolice #RIPEricGarner #RIPMike Brown," he continued before adding: "This May Be My Final Post."
Minutes before the attack, Brinsley struck up a conversation with two men, Chief Boyce said.
"He asked them for their gang affiliation; he asked them to follow him on Instagram; and then he says: 'Watch what I'm going to do.'"
He then walked past the patrol car with officers Liu and Ramos inside, circled it and, crossed the street and came up behind the car, Chief Boyce said.
He walked along the pavement before firing four bullets through the front passenger window, hitting both officers, and then ran.
Brinsley fled to a nearby subway station, where police said he shot himself in the head using his semi-automatic handgun.
Police departments in New York and several other cities were said to be operating on "high alert", fearful of copy-cat attacks.
The NYPD has suspended all auxiliary patrols for the time being, and police unions have told officers to respond to every radio call with two cars and to not make arrests "unless absolutely necessary", according to CBS News.
Forces are also monitoring social media for threats. In Memphis, Tennessee, a man was taken into custody after writing in a post that he was "driving to New York to kill more cops".
Meanwhile, the family of officer Ramos joined community leaders near their home in Brooklyn for a prayer vigil on Sunday.
His 13-year-old son, Jaden, wrote on Facebook: "It's horrible that someone gets shot dead just for being a police officer. Everyone says they hate cops but they are the people that they call for help."
Officer Ramos's cousin, Ronnie Gonzalez, said the family had already forgiven his killer.
Mr Gonzalez also said the family would not object to New York Mayor Bill de Blasio attending the funeral, adding: "We're not disrespectful. We're not going to throw him out and say: 'Don't be here.'"
The mayor has been criticised by unions over what they perceive as his lack of support and respect for the police amid the recent protests over the deaths of Mr Brown and Mr Garner.
Last week, the Patrolmen's Benevolent Association asked officers to sign a petition calling for Mr de Blasio to be barred from attending their funerals if they were killed in the line of duty.
And on Saturday night, several officers turned their back on Mr de Blasio as he entered a news conference about the shooting.

Sum:
The man who shot dead two New York police officers told members of the public to "watch what I'm going to do" shortly before the attack, police say.