How to stitch black leather without staining your thread

[JackAllred93]

So I finished up a small project that I had some scrap leather for and decided to make a lighter cover cause why not. Simple enough right? Afterwards, I cross-stitched it with red thread and my thread looks super dirty and got a lot of the black on it. I even let the stain dry for two days before I stitched it and it still came out pretty dark. I think maybe I got the sequence wrong and I punched the holes BEFORE I stained it and it left some in the holes but even after it sat for two days, when I went to stitch it my fingers turned black. I didn’t go overboard on the stain just enough to cover the material so I am curious what can I do to keep my colored thread from turning black. I can imagine what it would do to white thread but I have seen it done and the black was black and the white was white. I am sure there are many more people in here with more knowledge than me on this so any help would be greatly appreciated!