Short answer: ffmpeg -framerate 30 -i frame_%04d.png -c:v libvpx-vp9 -pix_fmt yuva420p -auto-alt-ref 0 -b:v 0 -crf 32 output.webm — or upload a ZIP to our free PNG sequence converter.

Export the frames with alpha

Export PNG with an alpha channel: in After Effects choose RGB + Alpha, in Blender set the film to Transparent and colour to RGBA. Frames saved as plain RGB have no transparency to carry over. Number them consistently—frame_0001.png, frame_0002.png—so they sort in order.

The FFmpeg command

From the folder with the frames:

ffmpeg -framerate 30 -i frame_%04d.png -c:v libvpx-vp9 -pix_fmt yuva420p -auto-alt-ref 0 -b:v 0 -crf 32 output.webm

  • -framerate must match your animation.
  • -pix_fmt yuva420p is what keeps the alpha. Without it the WebM is opaque.
  • -crf 32 balances size and quality; lower is better quality and a bigger file.

In our tests this setting gave a 30-second 1080p clip under 10 MB with clean edges. Adding -deadline realtime -cpu-used 8 -row-mt 1 encoded it several times faster at similar quality.

Check the result

Open the WebM in Chrome or Firefox on a coloured page, or extract the alpha with ffmpeg -c:v libvpx-vp9 -i output.webm -vf alphaextract -frames:v 1 alpha.png. A black-and-white silhouette means the transparency is there.

Without the command line

Zip the frames and upload them to the free PNG sequence to WebM converter: up to 900 frames and 30 seconds at up to 30 fps, and the result is checked for real transparency before you download it.