It's also the system that his IT staff ranked toward the bottom when asked about the health, supportability and flexibility of all the company's systems, he said.

"It's probably the single biggest system in Microsoft in terms of transactions and important company information," he said. The transition to running it in the cloud is well under way, he said.

Like most companies, Microsoft has struggled with some of the issues that moving to the cloud creates. Scott recommends, for example, making sure that CFOs are well informed.

"We've found awareness is half the battle," he said. CIOs should describe to CFOs exactly what moving to the cloud will cost and what kinds of cost spikes might occur potentially at different times of the year. At Microsoft, that was good enough to satisfy his CFO's need for predictability, Scott said.

In addition, using cloud services has different implications for chargebacks. At Microsoft, Scott forced all costs into two different categories. One includes costs that can be directly attributed to and thus charged to a business unit.