The Barcelona star gave answers for around half an hour after his father Jorge Horacio Messi was also questioned. After they were whisked away in separate cars, Messi's lawyer briefly spoke outside the courthouse No. 3 in Gava, an easygoing coastal town just south of Barcelona near Messi's residence.
"The Messi family has wanted that we act with transparency, clarity and with a sense of co-operation, and that is how things went today as well," said Cristobal Martell, Messi's lawyer.
"It was evident that there was little intent of committing fraud and a great willingness to normalize the situation with the tax office and to not get involved in a fierce battle with the state in an attempt to interpret the current tax regulations."
A complaint lodged by a Spanish state prosecutor in June said Messi and his father tried to conceal earnings from the player's image rights. The complaint alleged the Argentina international owed 4 million euros ($5.3 million) in back taxes from 2007, 2008 and 2009.
Messi's father made a payment of more than 5 million euros ($6.6 million) on Aug. 14 to cover alleged back taxes and interest. That payment led the court to decide that neither Messi nor his father needed to post bail.
Friday's hearing was to see if there are clear indications of illegality. If so, then the judge could recommend that the case be prosecuted, barring an out-of-court settlement.
If the case goes to trial and Messi and his father are found guilty, they could face a fine reaching 150 per cent of the amount of back taxes and a possible prison sentence.
In the complaint, state prosecutor Raquel Amado alleges that from 2006-09 Messi "obtained significant revenue derived from the transfer to third parties of his image rights, income which should have been taxed." The complaint says Messi "circumvented his tax obligations" by using shell companies in tax havens such as Belize and Uruguay.
Messi and his father have always denied any wrongdoing. They have received the backing of Barcelona president Sandro Rosell and former president Joan Laporta, who was head of the club during the years covered in the complaint.
Messi, wearing a suit but no tie, arrived looking relaxed at the courthouse an hour after his father.
Messi was hailed by a group of fans and curious passers-by that grew to around 50 people, including many children, alongside about 100 journalists and photographers.
Upon leaving the courthouse, several fans chanted "Messi! Messi!" and a few teenagers chased his car as it sped away down a sunny street.
The case has apparently not distracted Messi at work. Messi is joint-leading scorer of the Spanish league with seven goals. Barcelona plays at Almeria on Saturday looking to maintain its lead of the league.
The 26-year-old Messi is widely considered the best player of his generation after winning several titles with Barcelona and the highest individual award, the world player of the year, a record four years in a row.
Messi is rated by Forbes as the world's 10th highest-paid athlete. He reportedly earned $41.3 million to June this year, $20.3 million coming from his club salary and $21 million in endorsements.
The soft-spoken Messi had steered clear of scandal in his highly successful career.
Spain has been trying to crack down on tax evasion as it fights to repair the country's public finances amid a double-dip recession.
Finance Minister Cristobal Montoro warned football players in April they should make sure they are "comfortable" with their tax affairs. Last year former Barcelona player Luis Figo paid 2.45 million euros in taxes pertaining to image rights from 1997-99.