Unveiled in March as a potent tool to aid the bloc's modest credit recovery, the four-year Targeted Long-Term Financing Operations (TLTRO II) aim to lower corporate borrowing costs to induce spending and ultimately revive inflation.
Offered initially at a zero percent interest rate, banks could be paid up to 0.4 percent of what they borrow by the ECB if they meet targets for lending out cash to the real economy.
Struggling with ultra-low inflation, the ECB will offer the new loans every three months.
It has also cut its deposit rate deep into negative territory and is buying 80 billion euros ($90 billion) of assets per month with the aim of getting consumer price growth back to its target of close to 2 percent.
But surveys suggested that funding is a relatively low concern for banks, who are more worried about finding customers with viable investment plans and healthy market prospects.
Banks repaid 367.86 billion euros of loans taken out in the ECB's first TLTRO over the past two years, all of which was expected to be rolled into the new TLTRO facility.
Including the rollover, the 399 billion euro take up -- from 514 banks -- is below the 435 billion euros forecast in a Reuters poll.
The net new borrowing of 31 billion euros is unlikely to surprise the ECB, however: sources familiar with the process had said it was bracing for a new take up in the tens of billions, not higher.