If you're happy with her using this stuff and the money spent on it and are mainly concerned about organisation, I'd go through everything with her and "triage":
(1) clean up any items leaking, leaked-on or otherwise dirty or messy. Make sure everything has its proper cap/lid on. Throw out anything expired or damaged/unrescue-able (e.g., shattered powder eyeshadows, liquids with missing lids unless they can go in a different container).
(2) identify anything she won't use and throw it away, donate it, or repurpose it so it's no longer part of her "stash".
(3) identify any unopened items (e.g., duplicates, backups) and if she expects to use them then make a list to keep handy so she knows what she has and doesn't buy more duplicates. Put them away out of sight until needed.
(4) Identify the items she actually uses at least daily and put them aside for a "priority" location e.g., on a countertop, desk, or dressing table. If she shares a bathroom, some may go in there and some in her room depending on when/how she uses them. The size of this stash and the space she has will determine how to hold/display this; there are lot of options available. You might also suggest/get her a suitably-sized pouch or little travel cosmetics/toiletries case for items she wants to carry with her, if she doesn't have one already.
(5) The remaining items are probably the hardest part! If there are seasonal items she won't use until spring, those can go away similar to step 3 (and then the cold weather stuff goes away when warm weather stuff comes out). Items like nail polish, perfumes, "festive" color cosmetics, etc. that she only uses occasionally can go in a drawer or closet/wardrobe if there's no room for them to be out, but make there she knows what she has and where it is - ideally clear storage where the items are visible.
(6) Limit the intake so she doesn't get overwhelmed again!! Assuming she's buying and paying for these things herself, introduce her to concepts like Project Pan or Use It Up! challenges so she gets some idea of moderate and responsible consumption of these kinds of items and the need to limit overconsumption and waste. If you're paying, institute a rule where something new gets bought only when its equivalent is used up and the packaging disposed of. Get anyone else (dad, older siblings, grandparents?) who might buy beauty items for her on board with this plan.