Welcome to the forum, @annalex!
You haven't given us much information about your data or the specific command you're running, but I suspect you may be overlooking DADA2's quality filtering step.
This topic goes into that briefly, and wisely suggests you consult your denoising-stats.qzv to diagnose sequence loss issues. The paper gets farther into the details. There are also tons of discussions of how to select DADA2 parameters here on the forum. Try reading up on the process a little, and let me know if you have questions.
Good luck!