ANA InterContinental Beppu Resort & Spa
Rooms with private onsen

Officially tattoo-friendly
The public baths here welcome tattooed guests — source cited below.
The City of Beppu's official Enjoy Onsen guide maps 100 tattoo-friendly hot springs across the city.
Source: City of Beppu — Enjoy Onsen official guide — https://enjoyonsen.city.beppu-jp.com/onsen/100tattoo-friendly_beppuonsen_japan/. Policies can change; if a shared bath matters to your trip, check the source before you go.
Prefer to skip shared baths entirely? Every property listed here has a private bath — a reservable private bath or an open-air bath in your own room — so tattoos are a non-issue, and so is privacy. These properties in Beppu all have one:
Rooms with private onsen
Rooms with semi open-air bath
Rooms with open-air bath