Most of Kyoto's temples and shrines are genuinely welcoming to photography — it's a huge part of why people visit — but the rules aren't identical everywhere, and getting them wrong ranges from a quiet correction to a real problem depending on where you are.
Interior photography
Photography is very often restricted or entirely prohibited inside temple halls housing significant statues, painted screens, or other cultural properties — both to protect fragile artworks from repeated flash exposure and, in some cases, out of respect for active worship spaces. Signage isn't always in English; when in doubt, look at what other visitors are doing, or simply ask.
Gardens and grounds
Outdoor garden and grounds photography is almost universally fine, and is where the vast majority of Kyoto's classic temple photographs come from anyway. Tripods are a separate question — some gardens restrict them during business hours because they slow foot traffic through popular viewing spots; a few permit them during off-peak times specifically for photographers. Assume restriction unless you see it explicitly allowed.
Drones
Drone use over temples, shrines, and most of central Kyoto is heavily restricted or banned outright under both national aviation law and local rules protecting cultural properties and crowded public spaces — this isn't a grey area to test; assume no, and look specifically for a permitted location if aerial photography genuinely matters to your trip.
Photographing people
Photographing geiko, maiko, and other people going about their day requires real consideration — see our geisha & maiko etiquette guide for the specifics. As a general rule across Japan, asking before taking a close-up photo of a stranger, particularly in a work context, is the respectful default.