Can't Export Green Screen project in Media Encoder

If you render with an alpha channel the background is already removed.

If you render an alpha only and a color version of a video you can use Track Matte to remove the background. You can also use a bunch of other techniques. You'll get a better result than trying to key it again because you don't have any adjustments to make.  

H.264 is not recommended but here is how to do it using the Adobe Media Encoder. Add your comp - threw this one together with shapes and a light effect. Added to the AME, duplicated, then changed the render settings like this:

Here's how to set up Set Matte and Track Matte in After Effects. Everything I did is revealed in the screenshot:

Here is how to set up Set Matte in Premiere Pro:

Notice in all of the screenshots that I have shown the transparency grid and that the spotlight beam effect is very slightly visible in the transparency grid. It would be impossible to get that kind of detail if I had added a green background and tried to remove the green background in any app. The lighting effect is just too simple. Here's the shot in Premiere Pro composited over a night sky timelapse.

That subtle light beam coming from the moon to the silly graphic would be impossible if I had added a green background and tried o key an h.264 movie. The subtly would be completely lost. It is never a good idea to add a green background to a video so. you can remove it later. The only reason to ever use a green background is when you are filming something and it would be too difficult to generate a matte any other way. 

If you are at all serious about learning compositing and effects you need to spend a lot of time studying the techniques, formats and the basic principals involved. Just poking around the forums and watching a few YouTube tutorials by enthusiasts isn't going to give you much in the way of a useful visual effects education. 

That's exactly what I thought. If another piece of software has the ability to remove a green background it has the ability to use transparency. Your workflow does not make any sense. It's an amateur move that wastes time. You already have transparency. Use it. 

There are lots of formats that render smaller file sizes than the default Lossless preset. Storage is so cheap that larger file sizes should not be much of a problem. In 1993 I spend more than $20,000 for an Ultra SCSI storage array that was 80GB.  It heated up the office so badly that we had to put in an extra air conditioner. That's about $2 / MB. I just checked today and the average price of professional SSD storage is about 27¢ / GB. Enterprise storage, the best standard HD you can get is about 0.028¢ / GB. 

I strongly suggest that you spend some time studying about video compression. GoPro Cineform is free and really good. It will do up to 10-bit color and supports alpha channels. It is one of the smallest visually lossless formats. Right inside the Adobe Media Encoder presets you can find a bunch of other formats that support both higher bit depts and transparency. Pick one that suits your workflow. About 40% of my production renders use GoPro Cineform, another 10% is a mix of other formats requested by clients, the other 50% are image sequences, which, don't save any time, but when I have a comp that takes four or five minutes a frame to render and the client wants to change 15 frames in a 400 frame shot I'd rather just render the 15 frames that need changing.

If you must have the very smallest file sizes, and you ware willing to deal with a significant loss of edge quality and both color and motion artifacts that distribution formats like h.264 then duplicate the project in the cue and set one of the copies to render alpha only. You'll find the option at the bottom of the setup panel in the AME. I don't know any editing app that will let you key things out that cannot use an alpha only copy of the footage as a track matte to cut out the background.

I'm confused. What does trying to export a greenscreen project mean? I think you want to render your movie so that someone can key out the background later. That's not a very good idea.

There is never a good reason to export a movie with a green background so you can then remove the background. You have already gone through the work of creating some transparency to add the green so why would you render something that requires you to remove the background again. You either export with alpha channel so the work is done using a format that supports alpha channels, or you export a black and white alpha only copy and a color copy, without the green background because you'll get fringing and then the Alpha Channel only copy is used as a track matte for the source footage. I know you see stock footage with green screen plates added, but most of them don't key well because of color compression and it an amateur move. No production company would ever do that. 

I suspect that you set the background color of the comp to green (there is no specific green screen color anymore, has not been for years) so that somebody else or even you could key out the background later. That isn't going to work for most formats. Choose H.264 you will get a black background because the background-color does not render. Set the background color of your comp to any color and enable the transparency grid and you'll see the transparency, and H.264 and a bunch of other distribution formats do not support alpha channels, and you should not expect them to do so because media players do not render transparency. You can't see through a standard media player. You should also not be using distributions formats (MPEG - H.264 for example) as production masters either. The compression and color artifacts you get with intra-frame formats makes them just plain lousy for any reasonable production workflow. 

If you really need to render an h.264 movie, and you want to be able to remove the background layer then render two copies. You can't render an Alpha Only copy using the AME and h.264 so you'll have to render a DI (digital intermediate) using another format or better yet, use the Render Cue. There is an alpha only preset in the Output module. Use that, then use the Lossless preset for the color copy, and load them both in AME to render your H.264. Even better, pick a production format in the AME and just render with an alpha channel. You'll have to learn about settings and formats to set them up properly, but the options are there. GoPro Cineform, ProRez, and several other formats offer the option to render with an Alpha Channel. Some even offer the option of rendering an alpha only copy. That's the right way to do things.