As part of the deal, she accepted the charges and a fine of 50 per cent of the amount owed, more than 7.3 million euros ($A12.2 million).
She also accepted another fine of 438,000 euros ($A734,000) to avoid a three-year prison sentence, the judge said during the trial's first hearing.
"Do you recognise the facts and conform with the new penalties that have been requested?" Judge Jose Manuel del Amo Sanchez asked.
"Yes," Shakira responded.
Wearing a pink suit, matched with a pink handbag and sunglasses, she arrived minutes before proceedings began accompanied by her lawyers, amid a media frenzy.
On Thursday night, Shakira won two Latin Grammy awards in Seville.
Hips Don't Lie singer Shakira won two Latin Grammy awards days before her court appearance.
Previously, the Hips Don't Lie singer, who also has a second tax fraud investigation pending with Spanish authorities, had vowed to fight what she called false accusations.
The prosecutor's office was seeking an up to eight-year prison term and to claim back the taxes it says she owes.
It alleged that Shakira spent more than half of each of the years in question in Spain and was therefore ordinarily resident in the country.
It also said that a Barcelona property she bought in May 2012 served as a family home.
Shakira, 46, lived with former Barcelona and Spain soccer star Gerard Pique for 11 years and the couple has two children.
The singer, whose full name is Shakira Isabel Mebarak Ripoll, moved to Miami after their separation.
Spanish authorities have pursued other major celebrities over tax evasion including soccer players such as Portugal's Cristiano Ronaldo, Argentina's Lionel Messi and Brazilian-Spanish player Diego Costa.
All settled and paid large fines.
Bayer Leverkusen coach Xabi Alonso refused to settle and eventually won a trial against the tax agency.
Spain's Supreme Court last month upheld his acquittal.
