I know how frustrating knee pain is, and am so sorry for anyone coming here seeking advice for it's alleviation. I had pain in lotus/padmasana with my inner left knee for about two years, a decade or so ago. And, while it was frustrating as hell, I learned a lot about the practice - and myself - through this injury. (Injuries can be the best teachers!)
When I was teaching Mysore style Ashtanga from 2010-2020, I often saw this issue in students who had experience in asana before coming to study with me, that is, those who had gotten to the point of the practice where they were doing lotus/padmasana multiple times during every practice. Generally, their knees had began taking on too much torque from the hips during the posture for a variety of reasons, and that longterm micro-trauma ultimately resulted in knee pain.
I'd been practicing for about ten years before my own knee pain manifested, and it hurt and it was really frustrating. To have to "back off" was something that my assertive, pitta personality refused to even consider. And, for months, like a good pitta predominant person, I scoured the internet and complained to my teachers, and tried everything to "fix" the problem - from daily deep hip opening sequences on top of my Ashtanga practice, to glute and thigh strengthening PT movements, to deep tissue massage, cranio sacral therapy, acupuncture, chiropractic adjustments. You name it, I tried it ALL for about six months in my desire (attachment, raga, one of the kleshas or obstacles to enlightenment) to regain the progress I'd seemingly "lost."
Alas, no amount of hip opening, no PT exercises, nor strengthening the muscles in my legs, nor bodywork helped. My knee still really hurt every time I tried padmasana.
Eventually, acceptance (or maybe wisdom) kicked in, and I gave up trying to fix it. In other words, I backed off, and cultivated non-attachment/vairagya around any results or "progress" in my asana practice, and simply rested my knee and tried to just enjoy and nourish myself with my practice. I did do my full practice, and wouldn't skip the posture, but simply modified for about 6-9 months, so that the inflammation could subside fully. (I also did full body abhyanga almost daily, and recommend you do, too, with an oil that is cooling; coconut is good in the summer months as I write this, but ask an experienced Ayurvedic practitioner in your circle for a consult and recommendation of what oil you should use for your particular body type and season. Abhyanga is something most of us should be doing each day regardless of injury, imho.)
As the knee got less inflamed, I began slowly trying to bring my leg into lotus during the practice, but would never go "into" pain - because that would only bring back the inflammation, after all. Modify modify modify - and be patient. Padmasana may come back. Or, it may not. Let go. Really. Let go of the fruits of your actions and simply do your practice at a deeper level, with empathy for your body, and listening to the deep wisdom of the body, that works so hard to keep you in this plane of existence! Treat your body like a puppy that is trying to learn, and loves you unconditionally, too. In other words, don't kick or abuse it when it's not doing what you want it to do. And, I know from my own experience as a practitioner, that is something many of us tend to do in this practice.
Meanwhile. After the inflammation went down, which took about 6 months of completely backing off, I still couldn't get it beyond a certain point without feeling pain. But, one thing had changed: I began to notice that when I did urdva padmasana, it was much easier to bring my leg fully into lotus, and that there was literally NO pain when I did that posture. A mystery - why?!?
What I realized starting in that moment, and many times since, is that pattern recognition is key to much of this practice, and to moving beyond the inevitable plateaus - and injuries. What's nice about doing the sequence regularly and in a specific order is that you can really begin to see these patterns - and also their anomalies. Like my being able to do lotus upside down, but not right side up: that was an anomaly, and I noticed it because my mind had quieted enough around padmasana (finally!) - especially because I wasn't bringing myself into pain each time I did the posture. I'd accepted my current limitations, accepted what was and wasn't really trying to change anything. Vairagya. It's much harder to recognize patterns if your mind is occupied with thoughts about pain and injury, and with the raga/desire to "do the practice like I used to do it." Once I stopped striving, once I let go of trying to "get" the posture, I was able to settle my mind, its vrttis, enough to actually discover the path to healing.
And, so, from this place of curious openness, I observed what was happening when I was in urdva padmasana, and noticed that MANY things were happening in it that weren't happening when I was seated:
#1 I noticed my spine was VERY straight and engaged. No slumping or rounding of the spine at all, beyond the necessary bend at the cervical spine.* Not only was my spiny VERY straight, it was fully activated, and flowingly dynamic along the main nerve channel now at the end of my practice. To sustain the inversion sequence, my bandhas were also alive and engaged - not clenched or stiff, just awakened. And, I noticed this activation and dynamism within the spinal column/shushumna nadi, changed my relationship with my pelvis, too. I could feel more stable at my base and all along my spine, even though I was inverted, and with that stability, my hips were more....open. All because I was upside-down.
#2 I was breathing more slowly in the inversion sequence/closing than in the flowing vinyasa portion of the practice - thus, calming my mind more. When I'd do the posture seated, my breathing would unconsciously begin to speed up...I'd go into fight or flight mode in response to the pain.
#3 My drishti was down my nose and soft, quieted in the inversion sequence, and this drishti had been unchanging for many asana in a row, too. This calmed my mind further, which settled or alleviated residual anxiety within my body, too, avoiding fight or flight response. When I would do padmasana seated, I noticed I'd be staring at my knee in anticipation, willing it to feel better - generally not focused on drishti at all, but preoccupied with my thoughts. Seated, my back would hunch in anticipation of the pain, my eyes would lose focus, my breath would speed up....and like Pavlov's dog, I'd be in fight/flight/freeze even before attempting to try the posture - that is, the stimulus of the memory of the posture would create a conditioned fear response that actually changed the way I built the posture!
#4 This combination of very erect, straight spine, very calm, steady breath, very focused drishti in the inverted padmasana posture ensured that my mind was not as involved as when I did padmasana seated. My mind was, in other words, not caught up in the vrttis, the repetitive feedback loop/memory of "oh my knee hurt last time, will it hurt this time? I am afraid it will! And what a bummer if it still hurts! I'll just try it and see.... Nope, still hurts. Damn, I wish it would get better! I am bad at this, not really a good Ashtangi... How can I fix this?!" Yada yada yada, which triggered fight/flight/freeze.
(I don't like to quote him these days, because KP Jois was a teacher who hurt many students, but I must acknowledge, he did get some things right - and this statement is one of them: "The asana is correct when the mind is quiet." )
When I realized this epiphany around my fear response, the very next morning in practice, in the first seated padmasana, I came through to sit and sat very very very straight through my spine in dandasana in preparation, engaging gently through my legs, rooting within my pelvis from the crests of my sitting bones, and letting my spine rise up and hold itself up from inside with mula and uddhiyana bandha - vs tightening my hips and external rotators to keep myself erect (which is the propensity of anyone who doesn't regularly sit on the floor from childhood.) I settled my gaze softly onto a nether region a few inches from my nose. Immediately, I noticed that my hips relaxed a little bit, and my low back released some tension. Curious, and maintaining focus, and breathing slowly and steadily for several breaths, I tried to remain calm, and brought the foot into lotus...and could see that I had "gained" about 2 inches closer to my opposite hip/abdomen than the day before. Eureka!
Each day, I approached padmasana this way, gently going a hair or two closer in with my foot without pain. I still kept up with a few preliminary hip opening/PT stretches that really helped release residual hip tightness from daily living (and if you'd like to learn these, and more about my technique of rebuilding your feedback loop around injury in asana, I offer FREE virtual consulting to students who wish to learn more about my teaching methodology and who wish to study formally with me, in 30 minute increments during my upcoming "Office Hours", starting later this month.)
I set about rebuilding the feedback loop around the posture so that my fear response to pain didn't kick in - a fear response which would make me hunch my back in anticipation. Rounding my spine in fear, closing off the flow of energy which kept it erect, would subtly cause my my hips to contract in order keep myself upright! I also slowed my breath and actively calmed myself with a soft drishti down my nose in lotus each time, so as not to stir up the the fear vrttis.
After about a month of this, my lotus "came back" fully - in fact, even better than before. I came to realize what I'd been doing that was causing me to inflame the knee joint in the first place, and I used this method in a variety of other asana that were problematic to resolve those issues, too. And, this is how I ultimately taught lotus to students, too, taking the time with each one in the Mysore space to break down the specifics of prana management (because that is what we are doing when we are doing this practice) and the importance of spinal integrity in their asana practice. In fact, when our shala was open, we had very few students who experienced pain in their knees, and if they did, most folks would be able to resolve it with this method.
BUT. We must be able to accept that maybe some of us are not meant to do padmasana, through no other issue than the way our bodies are formed. Some folks femurs go naturally into internal rotation within the pelvis, making padmasana a challenge, and some have femurs whose propensity for external rotation makes the posture easier. (Note, in about 99% of people who experience ease in padmasana, triyangamukha ekapada paschimottanasana is much harder, and you will notice a similar patterning around the relationship between baddhakonasana and upavishta konasana, too. Very few practitioners can do both postures within these posture groups with ease - that is, ONE of them will always be harder - because the femurs are brought to the limits of both external and internal rotation therein, and we cannot get past the way our bones are made and integrate within our bodies. Or....
abhyasa-vairagya-abhyam tan-nirodhah Y.S 1.12
Finally, it's how we approach these so-called "limitations" that are the mark of a wise and seasoned Ashtanga practitioner - not how many spectacular asana one can do. Just enjoy your practice, and try to let it nourish you!
I hope this helps. I offer it freely as one of the many gifts that came to me from my own practice. Remember, there is no guarantee that it will work for you, but all you can do is try it, without getting too attached to the results. If you need more guidance, feel free to check in during my Office Hours, too. May we all find our way!
*Please note that not one vertebrae of your spine, including the cervical, should be on the floor in any of the closing/inversion sequence! You must be on the back of the skull and on your shoulder bones in urdva padmasana. NOT on your neck. If you do not have a solid inversion, if any part of your cervical spine is on the floor, do not try to build lotus inverted. Simply work on creating a straight and dynamic spine, breathing mindfully, slowly and deeply, and setting your drishti with strong intention and peacefulness in seated padmasana postures.