In particular it put aside €600 million to cover possible costs of misselling insurance in Britain.
Without the exceptional charges, net profit would have climbed 12.9 percent to €6.57 billion, but this still missed the €6.92 billion expected by analysts surveyed by financial data provider Factset.
Net interest income, a key measure of profitability from lending operations, rose by 8.9 percent to €32.19 billion.
"In 2015, we have delivered ahead of plan in the right way, growing revenues by improving customer service and increasing loyal and digital customers," Santander Group's Executive Chairwoman Ana Botin said in a statement.
The bank suffered less than its Spanish counterparts when the country's property bubble burst in 2008 thanks to its extensive international operations.
Britain remains Santander's top market, ahead of Brazil and Spain.
In Brazil earnings were hurt by the plunge of the real, but net profit still amounted to €1.63 billion.
The ratio of bad loans dropped to 4.36 percent at the end of 2015, down from 5.19 percent at the end of 2014.
It said a key measure of the funds it has to weather adverse financial events, fully-loaded CET capital, had risen to 10.05 percent from 9.65 at the end of 2014.
The bank aims to achieve a ratio above 11 percent in 2018.
Santander's shares fell 1.5 percent in early trading in Madrid while the main IBEX-35 index was down 0.4 percent.