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Question about an issue I am having with intonation.

StratoBlaster23

StratoBlaster23

Jun 20, 2025
56
285
#1
I recently purchased a new Fender American pro 2 Jazz bass. I am having an issue that is really frustrating with my new bass. Even though my intonation is very close and checks out between the open string and 12th fret, my bass just does not sound right. It is playing out of tune even though the intonation seems correct. Songs and riffs that are second nature to me do not sound correct at all. I put my Jazz bass away last night and pulled out my Stingray to play and see if the issue has to do with my playing/ears/amp EQ/bass EQ. Nope. That bass plays and sounds just fine compared to my Jazz bass. I had Sweetwater set up my bass before shipping it to me and it seems like they did a decent job. Please, any and all advice on how to remedy this situation would be greatly appreciated. I just want my new bass to play and sound the way it should. Thank you in advance!
 

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#3
I would set it up as if I'd just installed new strings. If you don't know how. See the Carruthers video's online for "Bass setup". I'd be looking hard at your witness points over the bridge and nut. All the basics really. Pics of your bass MAY help us put you in the right direction. But I'd start at step 1 and go thru the entire setup. Twisted string is a possibility. May as well check that before you start the setup.
 
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#6
Yeah you are going to have to go through all the setup steps to make sure everything is right. Proper nut slots cut and depth. Relief and bridge height. You are fretting the octave right? Not just using the open harmonic. It’s the fretting that octave and open is what you adjust. Now what can throw that off once set is a poor nut slots cut or saddle. That doesn’t allow the string to move freely and it hangs up while playing and causes tuning issues. Also really high action can cause tuning issues because the string bends out of tune when playing it. There are magnetic pull anomalies which can be bizarre and cause tuning issues.
 
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#10
IME everyone should adjust their own intonation because we all play and fret differently. So my bass may be slightly out for a different player. On paper it should be no different but its partly how its played so it’s ballpark at best if someone else sets your instrument up.
 
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#12
StratoBlaster23 said:
I recently purchased a new Fender American pro 2 Jazz bass. I am having an issue that is really frustrating with my new bass. Even though my intonation is very close and checks out between the open string and 12th fret, my bass just does not sound right. It is playing out of tune even though the intonation seems correct. Songs and riffs that are second nature to me do not sound correct at all. I put my Jazz bass away last night and pulled out my Stingray to play and see if the issue has to do with my playing/ears/amp EQ/bass EQ. Nope. That bass plays and sounds just fine compared to my Jazz bass. I had Sweetwater set up my bass before shipping it to me and it seems like they did a decent job. Please, any and all advice on how to remedy this situation would be greatly appreciated. I just want my new bass to play and sound the way it should. Thank you in advance!
Click to expand...

Are you matching 12th harmonic vs 12th fretted? Ignore the open string...for now.

Riis
 
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#16
pingvuiini said:
How close are the pickups to the strings??
Click to expand...

This. Start with easy stuff. Pickups that are set close to the strings can pull them out of tune, especially when you play on the higher frets, which drops the strings closer to the pickup.

I'd try lowering the neck pickup. The strings are tauter at the bridge pickup and are thus less likely to affected audibly by the pickup's magnetic field.

Count the number of turns of the screws, so that you can return the pickup to the original height if pickup height turns out not to be the problem.
 
#17
First of all, I believe @pingvuiini made the first mention of checking the pickup height. If either are too close, you’ll get weirdness that will include fretted notes sounding out of tune, especially notes above the 12th fret with the neck pickup being the one that’s too high.

The other thing to do is to verify intonation at notes other than the 12th fret. Intonation can look good at the 12th and get sharper at 15th, 17, & 19th fret. This depends a lot on which string (BEADG etc) with the lower pitch & larger gauge strings being more prone to the problem. What gauge you are playing & string action / height also have an effect.

The Sweetwater setup is just getting the bass in range of a setup for you. Them getting it dead on for your style of playing is not impossible, but unlikely. Neck relief is more critical than most players believe, and just a couple thousands of an inch can really change the feel of a bass, but neck relief and action need to be set before intonation. Setting intonation first and then raising or lowering a string a couple mm or changing the neck relief slightly will throw off intonation.

You just need to troubleshoot. If you have a tuner that displays frequency, it makes it easier and more precise to compare the chimed note at 12th fret to the fretted note at 12th fret. Using a tuner with a needle, scale, or lights usually isn’s nearly as precise as a tuner displaying the frequency down to 0.1 Hz
 
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#18
First thing i would do is free. Like others have said is check the pickup height. If strings are too close to the strings it could cause issues with intonation, or even sound like mild chorus. The closer the strings are to the pickups, the more the magnets pull on the strings and interfere with how they vibrate. Lower the pickups and see if it fixes the issue.

If that didn't work, i'd replace the strings. Strings could have been twisted on installation, or damaged in some other way. Make sure you don't twist or damage the new set. But, if you're having an issue intonating all your strings, my guess is it's the pickup height or something else. The odds that they damaged or twisted all of the strings on installation, or that they manufactured all strings with the same defect is pretty slim. Too-close pickups are across all strings.

If it's neither of those, ignore what i said and listen to someone who knows more than i do. 🤷‍♂️ :laugh:
 
#19
Intonation should not only be checked at the 12th fret. At least check at 7th and 5th frets as well.
Other string gauges may cure the problem. Slightly changing action and/or relief (trussrod) may cure the problem as well.
I, for myself, am not bothered with intonation above the 9th fret, as I seldom use the higher frets. 😁
 

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