Problem with knees after long bike ride

On recent cycle rides after a few hours of cycling the outer side of my right knee feels sore. I am think this down to lack of cycling, weight training and old cycle shoes or could be it be somthing else?

Could be the way you're turning your legs inwards (or outwards) due to lack of cycling or change in flexibility - possible solutions an up to date bike fit if you haven't had one recently, although they will probably do one of two things for that based on personal experience adjust your cleat angle to make the leg turn as it should and/or add a wedge under the insole to change the "drive" angle

If you dont want the expense of bike fit, you could perhaps try adding some flexibility exercises into your daily routine, perhaps those specific to the piriformis might be a good call and will open up the hips, changing the drive angle and in turn eliminating knee pain?

Anyway what do I know but it might help ITB

Try sitting on a table with your legs free to swing. Look at the way your feet (in cycling shoes) are - specifically the angles. Try to replicate the foot specific angle for the individual cleats - as Gastank says, it sounds like the way your legs are tracking. Easiest thing would be that your cleats could do with adjustment.

I had a similar issue and found that twisting one cleat out made a huge difference