You can absolutely connect to multiple company files, but there are a few things to keep in mind. First, if the QuickBooks Desktop process is running, then the currently open company file will be connected to. This is due to a limitation of the QuickBooks Request Processor, which we rely on for connecting and obtaining data. As the Request Processor is only able to connect to and expose one Company File's data at a time, you can not connect two company files simultaneously.

To work around this, you can set up QuickBooks with the QuickBooks Gateway (a.k.a. the Remote Connector) to switch between those files automatically. This can be accomplished by either leaving QuickBooks closed on the machine or by having the process running with no company file selected. You will also need to ensure that you have properly set up and configured the QuickBooks Gateway with multiple users, each of which will correspond to a different company file in QuickBooks.

Please also note that QuickBooks only allows access to a single file at a time. If requests are submitted to different files at once, the QuickBooks Gateway will queue up the requests and process them one at a time. This can be a big performance hit depending on the size of the company files, as QuickBooks must close the currently open file and open the new one each time you change the company file you are connecting to.