Ulf Wendel has a new post today with details on using stored procedures with mysqli - not overly difficult if you know how to handle the IN, OUT and INOUT parameters. He includes a few code examples showing how to use them.

Out of curiosity I asked another friend, a team lead, how things where going with their PHP MySQL project, for which they had planned to have most of their business logic in stored procedures. I got an email in reply stating something along the lines: "Our developers found that mysqli does not support stored procedures correctly. We use PDO.". Well, the existing documentation from PHP 5.0 times is not stellar, I confess. But still, that’s a bit too much... it ain’t that difficult. And, it works.

He describes the three parameters (IN, OUT and INOUT) and gives some examples of setting/getting them from your SQL statements. They're all still set up using the query method on your connection as well as handling the result sets that come back and working with prepared statements.