Is the zakat on a pharmacy calculated on the total value of goods and capital and then divided between the two partners, or is it borne entirely by the partner who is liable for zakat?

The company in which the capital of both partners consists of goods, or where one partner's capital is goods and the other's is a shop (real estate), is an invalid partnership (fasid); because it is not possible to return to the original capital or its equivalent. Therefore, it must be rectified by determining the value of the shop and the medications. Each of you should then purchase an undivided share from the other, and then agree on the profit margin.

As for Zakat, at the end of the year, you must gather your cash, assess the medications at their market value, and add any debts owed to you by others. Then, you subtract the rent for the shop and any debts you owe, and pay Zakat on the remainder if it reaches the nisab (minimum threshold).