Keeping the bunny litterbox clean is definitely key as that is where the smell will come from since bunny’s themselves don’t smell.
I like to use rosemary. We have a large bush in our front and back yard, and I use cuttings from that and put them in a basket. They last for a few days before they begin to dry out. But during those few days, I just can tear apart the cuttings and it offers a fresh scent.
I also put Basil and mint — just cut some off that up and wow….smells good.
You could also use baking soda in a container up and away from where your bunny can get to it. You can use the ones that are meant to go in the fridge — the side of the box opens up and there is sort of a cloth material that allows more air flow. I’m sure you could create someting similar.
I used to use natural sachets, filled with things that weren’t irritating to a bunny (citrus can be irritating), but Rose, Lavender, rosemary, hibiscus and I would hang it near a fan or on the door knob.
I’ve also heard of the a dish of vinegar and water mix working well. Though I haven’t tried that. A member a while back used a bowl of charcoal and that seemed to work well for her.
Out of everything though, a fan and keeping a window cracked for air flow is the best for keeping the “urine” amonia smell out. I am lucky though because the weather where I live permits that all year round, and our alarm system works even when the window is cracked a few inches (it’s based on movement of the window). So I can keep it cracked wide enough get enough air flow without compromising security either.
But if there are days when things have to be closed up, i just make sure to scoop up the urine in the morning and again in the evening. You don’t have to clean the whole box or anything — just scoop up the urine soaked litter, and put a new scoop of litter in. No biggie to do but it can make a big difference scent wise.