Staining Wood Filler Problems (How to Solve Them)

You may have tried staining wood fillers before. Wood fillers are best to seal the holes and patches on the wood. Staining preserves the original wood color, but staining over the filler can be tricky. 

Sometimes, the result of staining on the filler area doesn’t appear as you expect. So, you must find staining wood filler very difficult now.

Hence you might ask, what are the staining wood filler problems?

Well, the stain might not stay on the wood filler. It can wipe away after some time. The color of the stain on the filler can look lighter than actual wood. The stain on the wood filler can discolor or look patchy. Your sloppy work may result in an unpleasant-looking wooden piece.

However, if you don’t want to face any of these problems, we have this article for you. 

Without wasting any time, let’s jump right into the next part!

What Problems Can You Face While Staining Wood Filler?

staining wood filler problems

Staining wood filler is not an easy job. You can face some difficulties that you need to overcome. Remember, always test and experiment with different solutions before actually applying them to your furniture. 

Here are some most common staining wood filler problems you should be aware of-

1. The Stain Won’t Last

After staining the entire furniture, the stain starts to come off from the wood filler area. If you use a water-based stain, it doesn’t stick to the wood filler. Just one swipe and the stain disappears. 

Sometimes after one or two days, the stain vanishes from the wood filler.


Always use stainable wood filler for your wooden pieces. If that doesn’t work, change the stain. 

A water-based stain cannot penetrate the wood filler. It just sits loosely on the surface. 

Use oil-based or gel-based stains to solve the issue. Oil and gel-based stains can evenly penetrate the wood filler. In case you’re unsure about which stain to go for, here are our favorites-

You can choose your stain from here and get going. These stains take a long time to dry. But once they’re dried, the stain sits on the wood filler permanently. 

2. Stain on Wood Filler Lighter Than Other Areas

After staining, wood filler areas appear lighter than the entire furniture. As wood fillers are lighter in color than wood. Stains are semi-transparent, they don’t quite cover the filler area. 

So, when you finish staining, those filled places look highlighted and unpleasant.


Choose a stain one shade darker than the actual wood color. Apply a thin coat of that stain on wood filler. Give an hour or two to set the stain. Once it is set, observe the color. It should be close to the wood color.

If you are confused with the colors, do a test batch on a piece of wood. Keep experimenting until you are happy with the result. Then apply the final color to the furniture.

Now brush a stain that matches the wood color on the entire piece. Use a paintbrush to apply the stain. Use a foam brush or sponge to apply the stain to the entire piece.

Not sure which foam brush would be right? Here’s our recommended ones-

Once it’s done, the stained wood filler areas won’t stand out anymore.

3. Discolored Stain

The stain loses its original color with time. The stain on the wood filler looks greyish or ash.

This issue is seen in furniture made with softwoods. Like pine, maple, juniper, birch, redwood, spruce, and fir wood.


Use a pre-stain conditioner to avoid discoloration. Before wood filling any holes, apply a thick coat of pre-stain conditioner on the entire wooden surface. The conditioner protects the wood filler from being absorbed by the wood. 

After the conditioner dries, seal the holes with the wood filler. Apply another generous amount of conditioner before staining the filler. Let the conditioner fully dry before applying the stain.

This prevents the discoloration of stains on wood fillers.

4. Stain on Wood Filler Looks Patchy and Grainy

Sometimes the stain on the wood filler sits permanently. But, after drying, it looks grainy and patchy. The texture of the filler area looks uneven and feels rough.

It happens because of not sanding the wooden piece properly before staining it. If you don’t sand the wood before filling and staining it, the surface remains rough. Nothing sits well on a textured wood.


After filling the holes on the wood with wood filler, sand the entire piece. Use a sandpaper or sanding tool and give the wooden piece a smooth finish. This way, the wood filler will have a smooth surface.

Use a cloth to wipe away the excess wood dust after the sanding process.

Apply the stain after sanding the wood. The stain will sit uniformly on the wood filer. The texture will not be grainy or patchy. It’ll look even and feel smooth.

Sanding with sandpaper takes a very long time. As you have to sand a large surface, it’s better to use an electric sander. It is efficient to make the sanding faster and easier. 

We have a list of electric sanders for you, so you can sand the wood quickly-

Use one of these electric sanders and save a lot of time. 

We’re done with the solutions to the staining wood filler problems. This will make staining the wood easier for you now.

Frequently Asked Questions

Question: What to use to clean wood after staining?

Answer: It’s better to use a dry cloth to remove dust from stained wooden furniture. Don’t use any chemicals or water to clean. Water can damage the wood.

Question: Can we paint wood over the stain?

Answer: Yes, you can paint wood over the stain. You don’t need to sand the wood before painting. Use a stain-blocking primer as a top coat then apply your choice of color on the wood.

Question: What to put over the stain to conceal it?

Answer: After staining the wood, put varnish on it as a topcoat. Varnish gives you a glossy finish on wood furniture. If you want matte finish use tung oil. Tung oil is water-resistant and works great as a stain concealer. 

Parting Words

That’s all for today! Now you know the staining wood filler problems and how to deal with them. We hope you won’t face any difficulties while wood staining from now on. 

Until next time, have a great day!

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