The regulator uncovered serious failings in the way it offered financial advice from its bank.
The £12,377,800 penalty was handed out after the FCA found there was a significant risk of Santander UK giving unsuitable advice to its customers, its approach to considering investors' risk appetites was inadequate, and for some people it failed to regularly check that investments continued to meet their needs - despite promising to do so.
Santander agreed to settle at an early stage of the investigation so its fine was reduced by 30%. Were it not for this discount it would have been fined £17,682,730.
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Tracey McDermott, director of enforcement and financial crime, said: "Customers trusted Santander to help them manage their money wisely, but it failed to live up to that responsibility.
"If trust in financial services is going to be restored, which it must be, then customers need to be confident that those advising them understand, and are driven by, what they need. Santander let its customers down badly."
In agreement with the FCA, Santander will now contact all affected customers and, for any sales that were sub-standard, redress will be paid where due.
Because the value of the stock markets has risen since many of these investments were first made, it is likely that consumer losses - and therefore redress for some - will be minimal.
Customers who held a Premium Investment, which were promoted as offering a tailored service including to reallocate investments and rebalance portfolios, may get redress if they paid for a service they did not receive.

The FCA's investigation found that Santander UK had:
· Failed to make sure that its advisers were fully getting to grips with customers' personal circumstances before making a recommendation, including understanding how much risk they were willing to take;
· Failed to ensure that customers investing were given clear and not misleading information about its products and services;
· for Premium Investments, failed to carry out regular ongoing checks to ensure the investment was still meeting customer needs;
· failed to make sure new advisers were properly trained before being allowed to give investment advice; and
· failed to properly monitor the quality of investment advice which meant that, where poor advice was given, it was not always picked up.

The failings took place despite repeated communications and warnings about suitability of advice to the industry by the Financial Services Authority (FSA), the FCA's predecessor, and were uncovered by both a mystery shopping exercise and wealth management thematic review by the regulator.

When the FSA first put its concerns to Santander UK in late 2012, the firm immediately decided to stop giving financial advice in branches to prevent further problems occurring.