Board Thread:Theories and Speculation/@comment-3568954-20170629122631/@comment-734582-20170629200707

Nope2937 wrote: Anime-only feats don't count Even in the Manga-canon they came here somehow. The Boruto movie implies how: The Otsutsuki already had access to a Shinju and processed into the chakra pills.

Thus yes, it's entirely possible that Kaguya already had access to chakra, simply not as innate power. But the Shiju is still the origin of all chakra, even if the Shinobi world's one wasn't the first to be the origin.