so i just bought a trek crossrip to build endurance for mountain biking and figured it get clipped in. i always ride flats on my mountain bikes and have never used clips before. after about 4 miles being clipped in i could really feel it in my knees. i pulled over, adjust the cleats and got back on the bike. definately better but today (went for first ride on crossrip yesterday) i can feel it in my right knee. im in very good shape, lift weights, do plenty of mountain biking, so i dont think its anything along those lines. my main question is how do i properly adjust the the cleats so my feet are in the correct spot? ive read a few articles about marking the sole of the shoe to get the ball of the foot on the pedal but i think my main problem is more toes in/out positioning. any help would be greatly appreciated

I'm not an expert at dialing in cleats, but one thing you might check is how you naturally orient your foot (i.e., toe-in, toe-forward, toe-out) when you stand and when you pedal on your flats. If your cleats are forcing your foot into an "unnatural" position, you're going to feel it in your knees. The float in the pedal will allow some range of motion (typically between 0 to 7 degrees, depending on design), but that may not be enough to accommodate your natural posture.

Some folks argue that you want the cleat straight even if you naturally toe out, because that will "train" the knee to get closer to the frame (which is, in principle more efficient)… but it's sometime hard to teach old knees new tricks, and can do more harm than good.

I'm sure others will provide better advice. And it might help them if you describe where your knee hurts (back, front, inner side, outer side). Good luck!

Some folks do better with pedal systems which offer float. Others do better with no float. Flats can usually be considered no float. So maybe you are allowing your feet to move into positions which unnaturally flex your knees, or maybe you are fixing your feet into a position you don't naturally assume on your flats. So watch and feel exactly how you ride with your flats and try to duplicate that with your clipless.

It's also possible that with the clipless pedals you can now push and pull on your feet in directions not permitted with the flats, and your knees are not used to these muscular stresses. If so, take it easy with them and gradually build up to a proper clipless pedal stroke.

Stretching might be helpful.

You can only do so much with cleat position. Cycling shoes are notorious for providing little in the way of arch support. That can cause the foot to rotate longitudinally, which in turn causes uneven loading of the knee joint. This is especially true for people with flat feet. In addition, some people need wedges to keep the foot in the right orientation to evenly load the knee. Unfortunately, none of this stuff is particularly easy to figure out without the aid of a pro fitter.

hmm thanks for the replies. i managed to find something i think may be helpful. someone said to sit on a table and let your feet hang. see where your feet naturally point and try adusting to that. ill go for another ride tomorrow and see how it feels, maybe i just need to get used to it