Anime vs Manga: Where Does Onimai End?
The Onimai: I'm Now Your Sister! anime ran from January 5 to March 23, 2023, and spanned across 12 episodes
These episodes approximately translate the manga by way of the early-to-middle chapters—through Chapter 21 in the majority of timelines.

Chapter 21 ("Mahiro's First Day") from the Wikipedia chapter list has Mahiro register for middle school with friends Momiji, Asahi, and Miyo

Reddit fan discussions affirm the anime pulled material non-linearly and omitted some chapters (such as the amnesia chapter and others)
reddit.com

✅ So—where to resume the manga?
Begin reading from Chapter 22 (straight after Chapter 21). That continues you straight after the anime's storyline.

Some fans, however, suggest starting the manga from the very start, due to the anime's sporadic adaptation order.

Bonus: Manga Extras Not in the Anime
The anime also omitted some side-chapters and special content:

Amnesia arc
Gacha-game chapter
Blu‑ray bonus chapters such as mini‑chapters 1.25 and 18.75
These are welcome extras to look at, if you like character moments or daily life scenes.

Quick Reference Table
Source Anime Endpoint Manga Equivalent Recommended Start
Anime (12 eps) ~Chapter 21 ("First Day") Chapter 21 manga Start at Ch. 22 or restart from Ch. 1

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Where Does Onimai Anime End in Manga?

TL;DR
The anime concludes at Manga Chapter 21, with a school transfer plot.
For smooth continuation, start with Chapter 22.
For full context, including bypassed arcs, begin at Chapter 1.