Everyone of my students, who follows my advice and upgrades from a kit zoom to a large-aperture prime lens (that's a fixed focal length with a very low F stop, such as 1.4 or 2.0), discovers that their camera is consistently focusing in front, or behind, the critically-chosen focal plane. What's going on is the result of cumulative production tolerances, both in the lens and the camera body, adding up to a missed focus.
The manufacturers finally admitted this mass-production shortcoming, and most cameras made in the past few years have an additional feature: "auto-focus fine tuning", in the custom functions of the menu.
What we then do is run a series of controlled tests, using a target that includes a scale to measure the "depth" of focus inaccuracy.
Basically a vertical target with a ruled scale tipped at 45°, it's meant to be used with cameras that have a micro-focusing adjustment feature (pretty much every camera over $2K made today).
You align your camera (leveled on its own tripod) and the target at a reasonable distance (aim for 5X your focal length - bit of a challenge to those who forgot their metric system after junior high...), use your high-speed/high-price lens wide open, focus with the center spot on the target, shoot, and examine your result.
Using your menu, move the focus micro-adjustment numbers by large leaps, until, by iteration, you can zero into the best setting for focusing precisely on the center of the scale. Repeat with each of your lenses (wide open, zooms set at their longest focal length), and all your photos will be in focus from now on!
A few pointers: shooting tethered will make your adjustments much, much easier, as you'll have to examine a small section of your image at 100%! Lightroom makes this a no-brainer, with the advantage of setting a preset that will add a bit of sharpening and clarity to your images, to better discern the center of the focus zone.
A bit more disconcerting, you'll find that all your lenses and bodies focus on different planes.
Very important note: most of your high-speed/wide-aperture lenses will also shift the focus further back, as you stop them down - you need to test/note/re-adjust-while-shooting your settings both wide-open, and at F5.6 (they'll probably stop shifting at higher F-stops than this....)
I know, I know, WTF? Well, I make a strategic decision before I start: will this be shot all ambient-light/wide-open (one AF-FineTune setting), or will I be using strobes and working at F5.6 to F11 (second AF-FineTune setting)? I always carry my chart - different bodies give different settings for the same lenses, at different F-stops....
Forget about calibrating zooms with variable-aperture, or most old film lenses, as the auto-focus sensors in your camera will have such a hard time with them (or in any high flare situation) that your focus will jump all over the place...
Now start practicing your focusing skills in the field, assured that, at least, your camera's autofocus agrees with your image focus.
NEWS: I now use FocusTune, from Michael Tapes, for a more critical (and automated) determination of the optimum auto-focus adjustment for each lens, at each aperture! Highly recommended… see it here
Here're my settings for 2 different bodies, 2 different lenses, at wide-open vs. stopped-down apertures:
85mm F 1.8: +20 F 5.6: +18
50mm F 1.4: +18 F 5.6: -16
28mm F 1.8: +11 F 5.6: +13
85mm F 1.8: +14 F 5.6: +12
50mm F 1.4: +4 F 5.6: -17
28mm F 1.8: +13 F 5.6: +6
and the 24-70 zoom, while not having much of a focus shift with stopping down, has two different settings, depending on focal length, such as 70mm: +8 and 24mm: +17 - totally defeating the purpose of a zoom, to rapidly change from wide to tele