A website owner posted on Reddit recently in a genuine panic. They had used Google’s disavow tool to strip out a batch of backlinks, expecting a tidier link profile and a bump in rankings. The opposite happened. Their traffic fell, and the links they had thrown away turned out to be ones that were quietly doing their job.
The thread reached John Mueller at Google, and his response is worth the attention of anyone who owns a website or pays someone to look after one.
What Mueller actually said
Google has spent years steering people away from the disavow tool, so it raised a few eyebrows when Mueller confirmed that it “does have effects”, while noting that it “has its place and time”.
That is not the reassurance it might first appear to be. If the tool has real effects, then it can move a site in the wrong direction just as easily as the right one. Anything with the power to rescue a penalised site also has the power to wound a healthy one.
Mueller balanced this with a second point that matters just as much: disavowing a small handful of links will not knock a site out of the results. So the tool is neither a miracle nor a curse. It is a precision instrument, and the problems begin when people treat it as routine maintenance.
A quick reminder of what it actually does
The disavow tool tells Google to ignore specific links pointing at your website when it assesses your site. It does not delete those links or scrub them from the web. It simply asks Google to discount them.
It was built for one narrow situation: a site that has built, or paid for, manipulative links and needs to distance itself from them, usually after a manual penalty for unnatural linking. That is the “place and time” Mueller referred to. For the overwhelming majority of websites, that situation never arrives.
The mistake that keeps repeating
The Reddit case is a familiar one. Someone runs their backlinks through a third-party tool, sees a column of “toxic” scores lit up in red, and assumes every flagged link is dragging them down. So they disavow in bulk.
The catch is that those toxicity scores are invented by the tools themselves. Google does not publish a toxicity metric, and it does not endorse one. A link a tool marks as harmful is very often a perfectly ordinary link from a directory, a forum, or a small blog. Disavow enough of these and you are no longer cleaning up your profile, you are throwing away signals that were helping you rank.
The other version of this mistake is negative SEO paranoia, the fear that a competitor is aiming bad links at your site to sink it. In practice, Google is very good at ignoring random spam on its own. It does this automatically, for nearly every site, without anyone ever touching the disavow tool.
When disavowing genuinely makes sense
There are real cases, and they are worth being honest about. If you have received a manual action in Google Search Console for unnatural links, disavowing is part of the fix. If you or a previous agency bought links, whether from a cheap marketplace, a private blog network, or one of those “1,000 backlinks for £20” packages, and those links are still live, cleaning them up can be justified.
The common thread is intent. Disavow is appropriate when the bad links exist because someone deliberately built them. It is not a tool for tidying up links you simply do not like the look of.
When to leave it well alone
If you have never bought links, never had a manual action, and are working from a tool’s toxicity report rather than a genuine warning from Google, the honest answer is to close the disavow tool and walk away. The most likely outcome is that it costs you rankings rather than saving them.
This is where a proper backlink and authority audit earns its keep. Knowing which links actually carry risk, and which are harmless, is the difference between a considered decision and an expensive guess.
Your rankings have dropped — what to check first
If your traffic has fallen and your first instinct is to blame your links, Mueller’s own advice is a sensible order of operations.
First, review your disavow file and make sure it reflects what you actually intended, which may well mean emptying it. Second, check the timing against Google’s algorithm updates. A broad spam or core update around the same dates is a far more likely culprit than your links, and recovery from those can take months rather than days. Third, rule out the big technical problems. Not a stray canonical tag, but the serious ones, such as accidentally blocking your entire site from being crawled.
More often than not, the answer sits in one of those three places, and the disavow tool is nothing more than a distraction.
The sensible takeaway
Mueller’s comment confirms the disavow tool is real and consequential. That is precisely why it deserves respect rather than casual use. For most websites, the best link strategy is not deleting links in a panic. It is earning good ones consistently and trusting Google to discount the rubbish on its own. If you are not certain whether your own backlinks are helping you or holding you back, that is worth checking properly before you touch anything. Get in touch for an SEO audit and find out where you actually stand.
Graig Upton
Graig Upton is a UK SEO and Google Ads consultant with 23 years of hands-on digital marketing experience. Google certified in Ads, Analytics and Conversions, he has helped businesses ranging from local providers to national brands - including Nando's and Financial Times - dominate search and scale their leads. Based in Preston, working with clients across the UK.