How long should I be sore after a workout?
Hmm. Those are not places where I normally get too sore after a workout, so it's good that you're paying attention. Typically, for a really good workout when I've been working out regularly, I'm sore for about 2-3 days (with the third day being noticeably better than days 1 and 2). If I haven't been working out that regularly, I still start to feel a little less sore by day 3, usually, but sometimes the soreness can linger. If it feels like it's not completely muscle soreness, especially with your knees, I would try to do some of the recovery workouts and stretching and be very careful until you're certain you're just building up rarely-used muscles rather than doing damage.
What workouts have you been doing? There's a difference between muscle soreness and tenderness in your joints. Soreness in ankles and knees might be a sign of too much intensity or high impact.
I have that problem when I work out because my joints are pretty beat up from competative dance and soccer when I younger. Typically I try to avoid a workout that will put extra stress on what ever was stressed the day before to give it some rest and I ice. You shouldn't really be sore joint wise more than 2-3 days though.
Sore ankles, knees and shins could also be a cue that your form may be incorrect putting excess weight and pressure into those joints. Muscular pain usually peaks around 48 hours, and then should start to decrease. Be sure to incorporate the Recovery workouts and maybe also start the yoga program simultaneously! If you are new to working out or even if you have been your whole life if it is imperative you treat your body well when you are asking a lot of it!
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