The question is a bit vague, but the answer is yes.
In Thermodynamics and Physics in general, due to the conservation of energy, work is always a transfer of energy between different systems. So we have to talk of what systems we are thinking of.
Also, let's start with a simpler situation: consider just flexing your arm through your elbow, just like lifting an imaginary dumbbell.
We consider three systems: your upper arm (bones and muscles) your bicep and your tricep.
Phase 1: Flexing (accellerating)
Your biceps contracts and starts pulling your arm upwards. It is applying a force on it for a certain distance: it is doing work. Your upper arm receives of energy, which is manifested in kinetic energy, while your muscles is losing energy: it is
converting its internal chemical energy into the kinetic energy of your arm.
Phase 2: Stopping
Now to stop your fist from hitting your face, your triceps contracts, applying a force on your bones to stop them. Notice this time the force is resisting the movement: thus now the arm is losing energy (indeed, it stops) because it is doing work. The energy is transmitted into your tricep muscles, where it becomes heat.
In accelerating, your muscles do work on your body to get it moving; in stopping, they receive the same amount of work back. So work is being done. On the whole, (ignoring air friction and changes in gravitational energy), no work has been extracted from your body: you are just standing still again, slightly warmer.