A transparent QR code has no background fill, so the surface it sits on shows through between the dark modules. That is what you want when placing a code on a coloured product label, a dark poster, a photo, a presentation slide or packaging where a white square would look like a sticker someone forgot to remove.
Transparency raises one hard constraint: the surface behind the code must be light enough, and the modules dark enough, to preserve contrast. Most phone decoders expect dark modules on a light background. A black code on a pale pastel background works well; a white code on a dark photograph fails far more often. If your background is dark, place the code on a light plate or an inset white area rather than inverting the colours.
Export as PNG with alpha, or as SVG, to keep the transparency intact - a JPEG will fill the empty area with white and undo the whole point. Then test the finished composition, not just the code on its own: scan it over the actual artwork, at the actual print size, under the actual lighting.