The cleanest seats go to those who upgrade
How deeply your plane is cleaned depends on how long the turn is. A “turn,” in airline jargon, is how long the plane sits on the ground between flights. For quick domestic trips like shuttles from Dallas to San Antonio, this can be as little as 30 minutes. Cleaning crews remove obvious trash, wipe crumbs off seats, buff the lavatories and galleys, and restock supplies. This is why you sometimes find used wrappers or the last passenger’s boarding pass in your seatback pocket.
For longer turns, crews have time to empty out the seatback pockets and vacuum the floors. Generally that’s about the extent of the difference -- unless there was a major incident like a “service dog” mistaking the beverage cart for a fire hydrant. Sometimes the airline will delay a flight to get that mess properly cleaned. But your seats, tray tables, and armrests are still crawling with whatever bacteria is left from the previous flights.
The cleanest seats go to those who upgrade. Delta and United told The Wall Street Journal they cleaned all first and business class tray tables and windows with sanitary wipes between flights. So, rich folks, breathe easy.
Contrary to what you’d hope, waste tanks aren’t necessarily emptied between flights either. That’s all dependent on the capacity of the tanks, and how full they are. For example, an A380 has capacity for 554 gallons of human waste onboard, which means after a short flight, it probably isn’t getting emptied. Elsewhere, smaller planes will have their tanks pumped every time they land. (And, no, planes don’t purge their tanks mid-flight as urban legend might have taught you. The FAA has repeatedly had to issue statements explaining that any falling waste is the work of birds, most recently when a Utah woman blamed aircraft for a deluge of feces covering her driveway.)
Airlines do a more thorough scrub-down when planes stay overnight at an airport. Crews wipe down the armrests and tray tables and in-flight entertainment screens, vacuum the floors, and clean out the seatback pockets. Galleys and lavatories are also thoroughly cleaned, waste is removed, and blankets and pillows are replaced. The plane is like the equivalent of when you clean up for company, but not right after the maid’s been there. So take heed, germaphobes: That 6am departure is your best bet for a clean flight.