Can my landlord charge a pet deposit after the lease has already been signed?

Did you tell her beforehand that you had pets? Did the original lease say anything about pets? Generally there is a discussion about pets but I can see how it might not be discussed if the landlord had no reason to think you might have pets. (And you know that it is a subject that needs to be addressed - it is particular to you.) If the lease says no pets, then she could kick you out for violating the no pets policy and still cause you to have to pay the rent or charges or whatever for violating the lease. She does not have to give you notice to show up at your apartment and ask about dogs. She can come to your door just as anyone can. And, either she saw the dogs or someone mentioned them to her. She does not have to pretend she does not know or that it is okay. The fact that she allowed them to stay, even in violation of the lease, does not mean that she is prohibited from collecting a pet deposit from you. You are both working out a matter - your violation of the "no pets" clause. (And, is it really surprising she sees that the rug is torn and she wants a deposit?! Especially in light of the fact that you failed to disclose that you had pets?!) I am unaware of ANY place that does not require a pet deposit and allows pets. Moreover, most if not all pet deposits are nonrefundable because the landlord must replace the carpet more often than not because of pee and smells, and even if not replaced, the carpet must be cleaned more than usual and defleaed, etc. And, some apartments even charge a monthly fee between $10 and $25 dollars for pets because of the additional damage to the lawn for pee and the additional work of maintenance in cleaning up poop. So - you violated the lease. She is working with you to not kick you out for violating by taking a pet deposit. If you do not want to provide the deposit, you can move out and pay the penalties. (I have dogs and paid deposits when I lived in apartments. They only time I did not pay a deposit was when I rented a home from an individual.)

It depends on what the lease says about pets. I agree with my colleague that the landlord can show up at your door just like anyone else; under certain circumstances she can enter your apartment without notice.