Sitting for extended periods of time when you are not used to it is likely to feel uncomfortable or even painful. The pain signals are your body’s way of letting you know that there is too much strain (due to inflexibility) or not enough support (due to muscle weakness in certain areas).
If you find it difficult to sit without pain please don’t just push through it, instead work with your body to make sitting more comfortable. While you are gradually increasing the amount of time you can comfortably sit, you can switch out your sitting meditation, for lying down or walking meditation practices.
Painful Knees during meditation
If your knees hurt while sitting it is likely due to tightness in your hips, because of the reduced movement in the hips the knees end up twisting and gravity puts pressure on the tendons (read the article Are you forcing your knees for more details).
If you only need a little extra support, you can use pillows either under the knees or under the hips to lift them up a little higher. If your hips are very tight, and your knees are way up in the air when you sit down, try practicing baddhakonasana, upavishtakonasana, janusirshasana A, and thread the needle pose. This will help to release the muscles in the hips so that there is no tension in the knees while sitting.
Painful lower and middle back during meditation
The most common reason for pain in the lower and middle back is that the muscles up the sides of the spine are not used to being engaged for a long time. This can happen to people who have a tendency to slouch, or even just people who always lean into their chairs. A quick way to improve this is to try to sit slightly forward in your chair throughout the day for gradually increased amounts of time to slowly build strength. You can also try poses like shalabhasana or ardha shalabhasana to specifically target this strength. If you find you regularly have mild back pain try some simple back bending poses like bhujangasana, tiryak bhujangasana, and saral bhujangasana.
Painful upper back and shoulders during meditation
Sometimes the tension is a little further up the back, this is usually caused by tight shoulders and a closed chest (try this shoulder-opening sequence).
Pain here can also be caused by tension in the neck and shoulders because the head is both physically and psychologically heavy. If your head leans forward or tilts to one side, gravity will work with the weight of it and excess pressure and discomfort will come.
To help with this image you are pushing the crown of your head up towards the ceiling (it will feel unnatural at first but after some practice, you will re-find the neutral position). If your mind is very heavy (stress, anxiety, emotional turmoil), this can also cause the neck and shoulders to become overly tense or tight. If this is the problem you might benefit from some chest and heart-opening postures, followed by some lying down meditation.
The point of this article is to show you that whatever the reason for your discomfort there is a way to make physical improvements so that you can be comfortable in the future. If you really want to focus on deepening your meditation practice immediately, then switch out the position, and either meditate on a chair, lying down, or with a pile of pillows for support, but look into the reason that you are having issues.