The latest FOS data showed a further drop in complaints in the second half of last year taking the total received to 10,320, 12% less than the 11,715 received in 2015.
Bank of Scotland (620), Santander (578) and Barclays (448) were the most complained about institutions.
However, while Bank of Scotland and Barclays saw drops from 769 and 473 complaints respectively in the first half of 2016, Santander received 15 more complaints than in January to June (563).
Data from FOS also revealed that Connells and Santander were the most successfully complained about firms in the sector between July and December – both seeing 36% of complaints against them upheld by the regulator.
The Royal Bank of Scotland (34%) and Mortgage Works (34%) both also saw at least one third of complaints against them upheld.
However, the mortgage industry as a whole performed well in upheld complaints compared to the rest of the financial sector.
On average, 27% of mortgage complaints made to FOS over the six-month period were successful, much lower than the national overall average of 42%.
In the first six months of 2016, 45% of mortgage related complaints were upheld, with Legal and General (92%) and Connells (57%) the highest of those published.
Overall, the FOS took on almost 150,000 new cases in the last six months of 2016 – a slight decrease compared to the first half of the year.
PPI disputes fell although it continues to be the most complained about product with just over 78,000 complaints – making up over half of all complaints to the FOS.
The general insurance (up 5% to almost 18,000) and payday lending (up 22% to over 5,000) sectors saw notable increases in complaints over the period.
However, complaints about packaged bank accounts fell by around half to 9,100.
Chief ombudsman Caroline Wayman said lots of factors could influence the complaints the regulator received.
“There’s a widespread feeling that we’re living in unsettled times, and money issues are often at the heart of people’s concerns,” she said.
“At the ombudsman service, the data we publish often show patterns of volatility and change.
“PPI complaints are down, but there are some suggestions that this could be the calm before the storm. The FCA’s proposals – including the PPI deadline – are likely to heavily influence our complaints volumes,” she added.