The limits will come in from 15 November, and will apply where Santander identifies payments to cryptocurrency exchanges using mobile and online banking.
Customers will be restricted to a £1,000 limit per transaction, and a total limit of £3,000 in any rolling 30-day period.
These limits are applied per account.
Payments from cryptocurrency exchanges will still be able to be received into customers' accounts.
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In a statement, Santander said the move is in reaction to seeing in "a large increase in UK customers become victims of cryptocurrency fraud" in recent months.
It added that it will be making more changes to limit or prevent payments to crypto exchanges in the future.
Santander will also continue to stop payments being sent to Binance, following the Financial Conduct Authority's warning to consumers about this cryptocurrency exchange.
Customers can still withdraw any money they have with Binance into their Santander account.