In apple pie order means very neat, tidy, and carefully arranged. If a room, desk, set of papers, or tools is in apple pie order, everything is where it should be.
This expression has been in English for a long time, with examples going back to the 1700s. The exact origin is not certain. One common explanation is that it refers to the neat appearance of apple pies, especially when pastry strips or slices were arranged carefully in rows. Whether that story is exactly right or not, the phrase clearly came to suggest perfect order.
Today, it sounds a little old fashioned, but people still use it to mean that something is especially well organized.
- Her desk is always in apple pie order.
- Before the inspection, they put every file in apple pie order.
This is not about pies in modern use. It is simply an idiomatic way to praise tidiness and organization.