Staining Wood Filler Problems (The 360 Guidelines)

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, I have this article for you. 

Staining Wood Filler Problems: Step-By-Step

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:

Problem 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 my favorites:

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But once they’re dried, the stain sits on the wood filler permanently. 

Problem 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 the 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.

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

Problem 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.

Problem 4. The 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. 

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

Stained Wood Filler Before And After

Stained wood filler is a product used to fill gaps, cracks, or imperfections in wood surfaces before applying a wood stain.

The purpose is to create a smooth and even surface that can absorb the stain uniformly, resulting in a more aesthetically pleasing and professional-looking finish. Here’s a brief explanation of the process:

Before Stained Wood Filler:

  • Preparation: Start by preparing the wood surface. Sand the wood to remove any rough patches, debris, or old finishes that might interfere with the filler’s adhesion.
  • Selecting the Filler: Choose a wood filler that matches the color and type of wood you are working with. There are various fillers available in different colors to blend with different wood types.
  • Application: Using a putty knife or a similar tool, apply the wood filler to the gaps, holes, or imperfections on the wood surface. Press it firmly into the voids to ensure good adhesion.
  • Smoothing: After applying the filler, use the putty knife to smooth the surface and remove any excess filler. Try to level it with the surrounding wood as much as possible.
  • Drying: Allow the wood filler to dry completely according to the manufacturer’s instructions. Drying times may vary depending on the product used.

After Stained Wood Filler:

  • Sanding: Once the wood filler is fully dry and hardened, sand the filled areas along with the surrounding wood. The goal is to make the surface smooth and even.
  • Staining: Now that the wood surface is prepared and the filler has been smoothed out, you can proceed with staining the wood. Apply the wood stain of your choice according to the manufacturer’s instructions, using a brush, cloth, or sponge.
  • Finishing: After the stain has been applied, let it dry according to the recommended time. If you desire a more robust finish, you can apply a clear wood finish or sealer over the stained wood once it is completely dry.

Frequently Asked Questions

What to use to clean wood after staining?

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.

Can we paint wood over the stain?

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.

What to put over the stain to conceal it?

After staining the wood, put varnish on it as a topcoat. Varnish gives you a glossy finish on wood furniture. If you want a 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!

Kevin Smith

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