Can we say in between if we are in the middle of an action? For example:
The doctor told me not to eat anything after midnight. In the morning I accidentally ate a seed and recalled as I was in between [eating].
OP's usage would always be wrong. In a time-based context, you can only be "in between" two different things. As Jeremy says, you can be in between jobs/relationships, because this places you between the previous job/relationship, and the (possibly hypothetical) future one.
For a single instance of an activity that lasts long enough to speak of some particular moment while it's still ongoing, you can say you're in the middle of [eating].
As an aside, recall is more often used for making a specific effort to recollect some past memory or knowledge. In OP's context, remembered or perhaps realised would be more likely.
In general, you don't say that. For example, you might say you are "in between jobs" or "in between relationships", but you wouldn't say you're "in between working" or "in between dating". Even then, this isn't a terribly common phrase, but you would use it with nouns.
Also, your last sentence doesn't really work. Is it just part of a sentence? Or do you need to move some words around? Maybe you just meant "I recoiled" rather than "I recalled".
A better way to put it would be:
In the morning I ate a seed before remembering that I was meant to be fasting.
Fasting means "refusing to eat for some period of time."
In the morning I ate a seed even though I wasn't supposed to eat anything.