I bought clipless pedals this past weekend, never rode them before. On the 13 mile ride home from REI, everything was great, I noticed that I was getting more efficiency. I then did 20 miles on Sunday, same result, everything was great. Monday I didn't ride, but my legs were sore, probably from using different muscles. Tuesday I did my 24 mile commute and started developing knee pain and my legs were very stiff. I don't worry so much about the stiffness, but want to keep a close eye on the knees. Today I did the commute and both knees are sore just under the kneecap on the lower side.
The mechanic at REI put the cleats in the default position on the shoes. I've ridden almost 3k miles in the past year and never had knee pain, but I was placing the pedal under the middle of my foot, not on the ball where the cleats place you.
I'm wondering if I should move the cleats a notch towards the back of the shoe and see if it makes an improvement. Maybe if it does, then look at moving them back to where they are now after I get used to it. Any suggestions?
Thanks!
Jon

I think it's worth a try. I've seen at least one fitter, can't remember who, maybe Steve Hogg, on the internet who advocates a more rearward placement.

Speedplay Frogs .. their design has a lot of angular float..

your cleat may be forcing an unnatural Angle to be forced on your Knee joint.

Or just go back to platform pedals so you enjoy the ride without the knee pain.

The new position of your foot on the pedal gives you an effectively longer leg, and your seat height might need to be adjusted up.

I'd say this is most likely your issue. I'd try that before messing with any cleat positions. A poorly adjusted saddle is one of the leading causes of knee pain. When you come to a stop, if you can get more than the front portion of your foot to touch the ground while on the saddle, it's too low. I know that sounds counter intuitive, but try it.

If you were pedaling with the arches of your foot it will take a while for your muscles to adjust. I would also suggest a basic fitting to get seat height and fore/aft configured by someone who knows how to set you up. You could try asking the REI.

When you walk or stand do your feet point out, in, or straight? If they are not straight and your pedals have no float, then your feet are being pushed in an unnatural angle. I would also definitely check seat height as the others have suggested.

Saddle position is always a potential place where problems can occur. What's really new with a clip less pedal is that the foot is fixed at a rotation angle or only has a limited range of angles. These might not be in the acceptable range for your knee, and that can lead to pain and even to knee injury. Fitting systems use either a "Rotational Adjustment Device (RAD)" or other cleat-focused system to set the cleat angle at one that will not damage your knees. Without experience I would not adjust cleats myself. Maybe fore/aft, but only if I could make sure the cleat angle was not changed.

For setting up cleats the first time, why not get some help?

I'm surprised the shop selling the shoes did not offer assistance with setup.

Personally I fit my own cleats (with no previous experience) and it was not that hard. I followed Steve Hogg’s series on foot correction and cleat positioning, the first of the series can be found here: https://www.stevehoggbikefitting.com/...-arch-support/.

For reference I use the Shimano XC30 shoe, which is an SPD cleat, so that I can use the shoes on a spin bike when exercising at the YMCA.

For cleat positioning I did the following:
For the fore-aft adjustment I followed the Steve Hogg method and have had great success and no knee pain. I followed Method 2 at the following link: https://www.stevehoggbikefitting.com/...leat-position/. I would recommend Method 1 or 2, but probably not 3. To find the 1st MTP and 5th MTP use this method: https://www.stevehoggbikefitting.com/...w-their-nails/.

Next I set the cleat angle (toe-in/toe-out angle) to ensure that my heels did not hit the crank arm and that my feet were in-line with my knees. To do this:
1) sit on the edge of a table with the edge of the table touching the back of your knees so that only your knees down are hanging off the edge
2) Relax your legs and feet, put my knees pointing forward, and observe the angle of your feet relative to an imaginary straight line from your hips out through your knees
3) hold the shoe in one hand and the cleat in the other and twist the cleat angle until the shoe matches the angle of your foot, but the cleat remains pointing straight
4) loosely tighten the cleat bolts.
To test if I had the right angle for each foot, I rode the bike for 30-45 minutes and determined if I had knee pain. I did have pain in my right knee, because my toe-out angle is very extreme so I set the cleat angle as far as I could and that fixed the pain issue.

Since my toe-out angle was wide, I set the Q factor (controlled by the lateral position of the cleat on the shoe) so that the cleat was all the way towards the inside of the shoe. This resulted in my feet being towards the outside of the pedal and my heels clearing the crank arms. If you do not have toe-in or toe-out, you should set the cleat so that your heel is roughly 2cm from the crank arm while pedaling. Have someone stand in front of you and watch you as you pedal backwards to see if you knees are in-line with your feet.

Lastly tighten your cleat bolts and fill the hex holes with candle wax to prevent debris from making it hard to change your cleats later.

I didn't know Steve Hogg had such a good write-up on cleats, thank you!

Although not for everyone, this is why I like my Speedplays.

Cleat properly adjusted are the primary concern. Brand of pedal has less do to with it. Changing brands and find pain relief is just luck nothing else.
If you read this article. Scroll down to the cleat section I do not think you will find anything better on the internet for free https://bikefit.com/s-13-road-bikes.aspx
By the way I don’t think there is such a thing as the “default” position for cleats. If there is can you please define that for us?
Good luck