There is a small bicycle parking lot located next to the public restroom, and it's free. If you arrive before eight o'clock in the morning, you can take the main road, turn right in front of the temple stairs, and then continue straight. There will likely be a guard there who can point you in the right direction.
If you are here at a later hour, you can reach the parking lot by turning right onto the Chawanzaka route on the way up. Bicycles are not allowed on the main road between 8:00 and 19:00.
If that parking lot is full, or if you want/have a one day bicycle parking pass, or just don't want to pedal all the way up, use the Kiyomizu-zaka paid parking lot, which is open 24/7.