It absolutely will, no question whatsoever. You're going from one lossy format to another. You could encode to a ridiculously high bitrate so you don't lose as MUCH quality, but that would defeat the purpose of doing it to save space.
You could either 1) re-encode to H.264/mp4 and lose some quality to save some space, or 2) leave them as they are and zip/rar them into an archive to save probably a few megabytes at most.
You should definitely just use H.264/mp4 to begin with, though. It's just better, and YouTube likes it more.