I make them in ramekins all the time. Butter and flour the ramekins (or use cocoa powder to avoid any white dusting) for easy release. Alternatively you can serve them right in the ramekins. And yes, cooking time is a lot shorter -- I think mine cook for 12 minutes. I suggest a practice run.
The ramekins should work fine! You could always do one on its own to test the cooking time before baking the whole batch. My advice would be just to start checking for doneness early. And flourless chocolate cakes are always delicious when the middle is a little underdone...
I work in a bakery where we make small flourless chocolate cakes baked in silicon molds. They come out adorable and really, really delicious. We bake them at 300 and start checking them for doneness at 18 minutes (my boss likes multiples of 6...) I don't know what recipe your working with, but they will bake a lot faster then a big cake. They should feel done around the edges, but still quite soft to the touch in the center.
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