The announcement from such a financial big-hitter will stimulate interest among IT leaders in Microsoft's Web services initiative.
Microsoft's .net technology, based on the concept of software services on demand, has been criticised for being over-hyped and hard to understand.
Analysts said that the HBOS project showed that large companies were using .net technology to integrate tangled back-office systems.
HBOS said Microsoft's .net technology would allow its customers to access their corporate account details online for the first time.
The bank will use .net to modify an existing corporate banking system from Bank of Scotland which can only be accessed through dedicated PCs.
Dermot Grimley, head of the HBOS e-commerce development centre in Belfast, said, "Key factors in the project are security, performance, functionality and resilience. We needed a state-of-the-art architecture that was going to be available in five or 10 years' time."
The flexible architecture of .net would also make it easier for the HBOS IT development team to add new features to the corporate banking system when required, Grimley added.
The new system is due to go live in November.
Last month clothing retailer Marks & Spencer announced that it planned to base a new fraud detection system on Microsoft's Visual Studio .net.
Steve Barrie, lead analyst at Bloor Research, said, "Companies can use .net technology to pull back-office systems together that have been developed in different development environments, for instance different versions of Visual Basic."