The Jaguar, Mustang, and Jazzmaster—sometimes called the Fender ‘offset’ guitars have individually adjustable saddles for setting each string’s intonation. The basic principles are as usual so let’s recap the prerequisites.

The rest of your setup must be right for you before you start. Intonation is the last thing to set so get your action, relief, nut and pickups sorted out first. You should have fresh strings (of your usual gauge and brand) installed, properly stretched, and tuned up as normal.

Remember, always check intonation and tuning with the bass in the playing position (i.e. not lying on a table or counter but upright as if you were playing it).

The basic theory, as always, is this:

Pick the open string and verify it’s in tune.
Fret at the 12th fret and pick this note. Compare it to the open string—is it flat or sharp?
If the 12th fret note is flat, move the saddle forward a little using a flat or philips screwdriver as appropriate.
If the 12th fret note is sharp, move the saddle back a little by turning the screw clockwise.
Retune the open string and go back to 1.

Jazzmaster/Jaguar Bridge -Intonation by adjusting screws at rear

Mustang bridge - intonation by adjusting screws at rear

FLOAT THE BRIDGE IN THE RIGHT POSITION

Your Jag/Jazz/‘Stang bridge is designed to ‘float’. The bridge is intended to stand on its height-adjustment screws in the ‘thimbles’. The idea is that tremolo-use would rock the bridge back and forth so the strings wouldn’t have to slide across the saddles and tuning stability would be improved. For the most part, this works (as long as you’re not dive-bombing it).

Do remember, though, that this means you must set intonation with the bridge in the ‘proper’ position.

For most people, this means the bridge is sitting in the centre of the thimbles—at right angles to the body—with room to rock backwards and forwards.

Comparison of bridge 'orientations' for Jaguar, Jazzmaster, Mustang

OR FLOAT THE BRIDGE IN THE ‘WRONG’ POSITION

That said, there are players (and repair people) who like to push the bridge against the back of the thimbles so it’s ‘default’ position is angled towards the back of the guitar.

The advantage of this is that there’s a positive stop point. If you ever feel that your intonation or tuning is out, you can give the bridge a nudge backwards to ensure it’s where it’s supposed to be. The disadvantage is that, while down-bends on the trem will rock the bridge, up-bends mean the strings move across the saddles (which is what Leo was trying to avoid).

In practice, I don’t find any major additional tuning issues with the bridge angled back so, if you want to try it, go for it.

Whichever way you choose, set your intonation with the bridge in that position and, if you change, you’ll have to reset intonation.

JAGUAR/JAZZMASTER/MUSTANG INTONATION QUIRKS

If your bridge floats upright, give things a check every now and then to ensure it’s returning where it should. You’ll likely notice tuning issues if they occur when you're actually using the trem but, if you don’t use the trem much, your bridge might get shifted to angle back or forwards without your realising. Keep an eye on it.
Some offset guitars now come with tun-o-matic bridges installed. No problem. Check out the tun-o-matic intonation instructions.

BRIDGE UPGRADES

The standard Jaguar/Jazzmaster bridge isn’t brilliant. It’s got threaded-bar saddles that aren’t great for tuning, or for holding strings. The height adjustment screws in the saddles can often vibrate loose, rattling about and messing things up.

If possible, a lot of players swap in a Mustang bridge instead. The Mustang bridge is a bit more solid. It’s got brass ‘barrel’ saddles with a preset radius and no individual saddle height adjustment. The problem is that, as standard, it only comes with a 7.25” radius. Some Jags and Jazzmasters are fine with this but some have the more modern, 9.5” radius on their fingerboards.

Warmoth sell a ‘Modified Mustang’ bridge with some saddle height adjustment and this can be a good option. StayTrem also make a Mustang style bridge that is available in either 7.25” or 9.5”. They’re nice bridges

MASTERY BRIDGE

And of course, there’s the Mastery Bridge. This is a redesign of the original offset guitar bridge that’s pretty well thought out. It doesn’t float in the same way as the original but the enhanced coupling and the bridge’s solidity make for good tone.

Setting Intonation On A Mastery Bridge

The Mastery bridge has two saddle-pieces, each holding three strings (one for wound and one for unwound). Each saddle-piece is adjustable for overall angle rather than having each string adjustable.

Two screws on each saddle-piece alter its intonation angle. Since you’re adjusting the overall intonation of three strings, the Mastery intonation may not be as ‘exact’ as if each string were individually adjustable.

That said, because we have one saddle piece for wound and one for unwound strings, in practice, it’s pretty good. If you play with a wound G string, you might have some difficulties balancing that string's intonation but I suspect that’s a pretty small percentage of readers.

Here’s how I set intonation on a Mastery.

Set your intonation for the first string.
Then set the third string intonation.
Check the second string intonation. If all three strings are pretty close, you’re done. If one is out, you can adjust the overall angle to ‘balance out the differences’ in the same way you might for a three-saddle Telecaster.
Follow the same pattern with the wound strings (4, then 6, then 5)