Apotheker is a story-driven logic puzzle game where you use tools and ingredients to craft potions. As the game progresses, you meet NPC's who visit your store front and offer unique quests and special rewards. You also unlock new ingredients and tools, which give you more options as to how to complete your potions. It features different difficulties, ranging from experiment which allows for ample testing and retrying of potions, to expert, where all decisions are final.

After inheriting your grandmother's old shop, you must learn the subtle art of potion-making. As you collect money and ingredients needed to make the Elixir of Life to save her, you will also encounter various citizens of Rheinwall, who will help you on your quest to save Grandma.