VAT: the platform usually handles it
For app-store and marketplace sales to consumers, the platform is usually the deemed supplier. It charges the consumer's local VAT and pays it over. Your own supply then becomes a business-to-business supply to the platform, with VAT reverse-charged. Sales made directly from your own website fall under the OSS scheme. See the OSS for digital services. Write down once how you treat each type of income: store sales, direct sales, advertising and in-app purchases. With this record, you avoid double counting later.
Income tax: all income is taxed in the BV
All of it counts as business profit in the BV. Up to €200,000, the rate is 19%. The part of the profit that comes from your own technology can fall under the 9% innovation box. See the innovation box. Foreign platforms sometimes deduct withholding tax in their own country. Under the tax treaties, you can reclaim that tax or set it off against Dutch tax. The United States is the most common case. See the Netherlands-United States tax treaty.
Planning ahead
Put a holding company above the app BV from the start. With a holding in place, you are ready for a later sale. See a holding before a SaaS exit. During the growth years, set your own salary and any loans from the BV with care. See the founder's salary. Check the income overview every January, because stores change their terms.