There were 1,939 new home loan cases taken on by the FOS in the three months to November 2019, up from 1,793 received in the previous quarter.
Mortgages were the sixth most complained about financial product, with payment protection insurance (PPI) topping the list.
Payday loans, current accounts, credit cards and car insurance were also in the top five.
Only around 19 per cent of PPI complaints were upheld in the latest quarter, however, 62 per cent of payday loan cases were upheld, 48 per cent of current account cases and 36 per cent of credit card cases were ruled in favour of the customer.
In the current financial year to date, the FOS has received more than 14,000 enquiries about mortgages and took on around 10,000 cases.
By comparison, there have been almost 270,000 enquiries about PPI, with just over 180,500 new cases.
Last year the Financial Conduct Authority (FCA) set a deadline of 29 August 2019 for consumers to submit complaints about PPI.
But the ombudsman service said is now hearing from consumers who are unhappy with their provider’s final response.
The number of complaints about PPI dealt with by the ombudsman has now surpassed two million.
Caroline Wayman, chief ombudsman and chief executive of the FOS, said: “The ombudsman service has been receiving a significant number of complaints from consumers about PPI since 2011.
“There has never been another complaints issue on the same scale as PPI, and the volumes of complaints made to financial businesses around the deadline last August were truly unprecedented.
“We’re pleased that most businesses are now following our well established approach and paying compensation straight away.”