This ceiling may be attached directly to the rafters in which case there is little space between the paneling and the roof panels for mold to grow. An alternative is a scissor truss that leaves more space between the ceiling and the roof panels, but is still unlikely to pose a mold problem. For one thing the scissor truss should have venting in a gable end. Either way once the roof was replaced the leak should have ended. No more water no mold growth.

Your ceiling looks to have a natural finish (no stain) so should be cleanable. It's not a simple job, but it is DIY doable. It does require some supplies and equipment. You will need: oxalic acid from a hardware store; plastic bucket; plastic or wood stir stick; sponges; a spray bottle; vinegar; stainless steel scrubber sponge; an 8 foot or taller ladder (depending on the height of the ridge) or scaffolding; plastic drop cloths; goggles, gloves, mask, old clothing.

Oxalic acid is fairly mild but is still caustic, so wear old clothing that covers your skin. Protect your eyes, face and hands. Protect your flooring, counters, etc with plastic drop cloths. Open windows and use a fan to keep fresh air moving into the area. Take a break if you feel light headed.

Mix the oxalic acid per the manufacturer's instructions. Do not use metal containers or utensils. Climb the ladder, dip the sponge into the acid and apply it evenly to the stain. Let the acid sit on the stain for the manufacturer's recommended time. Use a clean sponge and plain water to wipe the acid off the wood. If the stain has disappeared, mix 1 part vinegar to 2 parts water in a spray bottle and spritz the ceiling to neutralize the acid. Allow to air dry. Should the stain still be noticeable repeat the process until satisfied. Once the stain is gone and the wood is completely dry, you should lightly buff the area with a stainless steel scrubber sponge. This should remove any trace of the process and smooth the wood surface.

If you want this to be a simple job, use a stain-block primer and paint.

Thank you so much! This is incredibly helpful.

I wouldn't bother w/the acid technique. just refinish the wood. sand it, stain it, and top coat it.

Sanding should even out those water stains to where a new stain would take and blend.

I'd prob go a tad darker and paint the beams white or black.

Or, do the reverse. refinish the beams, paint the ceiling portion

Here's the look I like. slightly darker wood ceiling, and darker beams.

Your ceiling planks could be very similar to these. I don't really like the brown beams, I'd do white or a black, or, do the beams in the same stain.

If you kept the trusses natural and painted the ceiling white:

if you completely refinished and darkened both:

kind of digging the ebony stained or dark charcoal painted option too.

there's no wrong answer here. It all depends on your style and what you like.

cool, thank you! re: sanding and staining - if the water stain is from a roof leak, could it be likely that the stain is all the way through and that sanding won't get rid of it? (roof is fixed)

Often, diluted regular chlorine laundry bleach (Chlorox) will remove water stains from wood. I would try it before moving onto oxalic acid.

How extensive is the staining? I think I see a small amount next to the nearest truss in the photo. Is that all there is?

If so, I would be tempted to just live with it vs possibly opening a can of worms that ends up in having to refinish the entire ceiling. That is, try lightening up the stain w/ bleach and seeing the results are good enough to live with...

If you decide to paint , make sure the primer you pick is shellac based. Zinnser Bin is shellac based. It will say on the can. I really hope you are able to keep the wood though, because it is beautiful.

hard to say. you'd have to try sanding a portion and see if the stain is all the way through.

Redoing that ceiling is a huge job. you're not DIY'ing it are you? call in a wood restorer and they'll take care of it.