The bank, part of the larger Lloyds Banking Group, was the subject of 927 new complaints in the first six months of the year.
The ombudsman said total complaints about Bank of Scotland were 15% down on the second half of 2012 and that 30% of these cases made against the business were upheld.
Santander was ranked second for mortgage complaints, attracting 774 in the six months to June while Northern Rock (Asset Management), which holds the toxic loans made by the former Northern Rock bank, saw a 32% spike in complaints and was third in the table on 676.
Barclays and Nationwide completed the top five with 397 and 331 cases respectively. Across all mortgage lenders the proportion of complaints upheld in favour of the consumer was 26%.
The Bank of Ireland, which controversially raised the differential on some of its tracker mortgages in this period, attracted 250 complaints.
Lloyds was the most complained about institution when looking across all categories with a total of 129,293 cases against it.
Complaints about Payment protection insurance (PPI) accounted for almost 90% of cases raised with the ombudsman in the first half of the year. A total of 266,228 complaints were lodged about this subject in the first six months of 2013, considerably up on the 211,885 received in the second half of 2012.