The Spanish bank said in a statement that its net profit fell by 14 percent to 1.46 billion euros ($1.7 billion) in the period from July to September.
That fell sharply short of analysts' expectations for a quarterly profit of 1.87 billion euros.
Santander explained that it "incurred a number of one-off charges, including a 300-million-euro charge relating to the integration of Popular".
Excluding this and other extraordinary items, as well as exchange rate fluctuations, "underlying profit increased by 14 percent to 5.6 billion euros," the bank said.
READ ALSO: Spain puzzled by Banco Popular takeover
Santander bought Popular at the beginning of June for the symbolic price of one euro to help avert its looming collapse.
Banco Santander nevertheless confirmed its full-year targets, saying it was continuing to pencil in "double-digit earnings per share growth for 2018".
"Our business has delivered another solid quarter of results -- with positive trends and further improvements in earnings quality across all of the markets in which we operate," said chief executive, Ana Botin.
Looking ahead, "we see significant potential for further profitable growth across our business and remain confident that we will meet all commercial and financial targets," she said.