Estonian limited companies looking to acquire payments online can apply for a merchant account with Stripe, Braintree, Decta, Paysera, Paddle and many more.
Please note that some of these companies may still reject companies that have directors or shareholders who are not physically located in Estonia or the EU. Restrictions could also apply to eligible industries. Be sure to check the terms of service before applying.
Do not expect any special treatment for being Estonian e-resident. For these companies you are a non-resident director and you can only hope that they accept you managing your company remotely. Stressing that you are official Estonian e-resident would not help you in any way. Mot of these companies have their own policies that do not sync with Estonian government efforts to provide remote company management tools to non-resident entrepreneurs.
PayPal is one of the companies that might ask you to prove your address in Estonia by a utility bill issued to your company. If you are Estonian e-resident not having an office in Estonia you might want to try with other companies first. Their lack of customer support and account freezing is legendary by now.
If you are asked for a proof of address of your company you might do ok with electronic registration certificate or a certificate showing shareholder information. You can generate these for free via Estonian Business Register.
If you are looking for an utility bill issued to your company please find our advice here.