Dressed in a dark jacket and white shirt, the 26-year-old Argentine international made no comment before or after the closed-door hearing on Friday at a court in Gava, the coastal suburb of Barcelona where he lives.
Testimony by the four-time winner of the FIFA World Player of the Year award revealed his desire to resolve the matter, Messi's lawyer, Cristobal Martel, told reporters after the hearing.
"It showed little intent to defraud and great intent to resolve the situation with the tax office instead of entering into a bitter battle with the state," the lawyer said.
Crowds of reporters and fans gathered outside the court where first Messi's father Jorge Messi and then the player himself were quizzed on charges of evading tax on the striker's image rights to the tune of €4.16 million.
They have denied wrongdoing, pointing the finger at a former agent of the player.
The court said Jorge Messi paid the tax authorities five million euros in August -- the 4.16 million euros claimed by the taxman plus interest -- which is likely to significantly reduce any sentence should they be found guilty.
Lionel Messi's form on the field has scarcely been affected, with the Barcelona forward scoring 10 goals in just seven matches this season as the Spanish champions remain unbeaten.
"I am not worried, I'm always on the sidelines of all that, just like my dad. We have our lawyers and our advisors who handle these things. We trust in them and they will solve the issue," he said in July.
Argentina coach Alejandro Sabella also appeared unconcerned , calling up Messi for next month's World Cup qualifiers despite having already secured a place at the 2014 finals.
Neither do Messi's legal problems appear to have tarnished his image among Barcelona fans.
"What I want is for this to be resolved quickly so Messi can relax and focus on the football," said one fan outside the court, Joaquin Bosch, 60, wearing a Barcelona shirt.
The case began in June when a prosecutor accused the Messis of evading tax by ceding the player's image rights to "purely instrumental entities" in Belize and Uruguay.
According to the prosecutor's report, Messi "obtained significant income" from image rights between 2006 and 2009 for which he failed to pay required taxes.
The news caused astonishment in Spain where Messi is seen as a more humble figure than other football stars, particularly his Real Madrid rival Cristiano Ronaldo.
"He has a very professional image, of being focused on what he does and very close to the public," said Carles Canto, a marketing expert for IMG Consulting.
Despite the initial consternation, the player's popularity doesn't appear to have diminished.
"Messi's image amongst Barcelona fans is so solid that it is very difficult for it to be clouded by this case," said Enric Baneres, a sports journalist for Catalan daily La Vanguardia.
"Tax evasion is something so common in Spain, like the siesta or paella, that the people are very permissive with it."
According to a document sent by Messi's father to the court, obtained by Catalan daily El Periodico, his former agent Rodolfo Schinocca was put in charge of organising the "structure and management" of the income from Messi's image rights.
Schinocca told Spanish radio station Cope that he had nothing to do with the case because he stopped working with the Messis in 2006, before the supposed offences took place. He accused Jorge Messi of wanting an offshore account to manage the income from the image rights.
While Messi's 323 goals in 387 games for Barca have made him irreplaceable on the field, his income from endorsements off it has also soared.
Between 2007 and 2009 he earned more than €10.17 million in image rights. US magazine Forbes lists him as the 10th highest paid sportsman in the world with an annual income of $21 million from endorsements alone.
Despite the court case, Messi continues to lead advertising campaigns for brands like Adidas and video games maker EA Sports. Its latest version of the immensely popular FIFA game franchise was released in Spain the day before Messi was due to appear in court with his picture on the front cover.