I am making a recipe for red velvet cookies with marshmallows on top. I use homemade marshmallows on top that are always very soft when cutting and very sticky, however I have noticed when I put them on top of the cookie and bake them they turn a nice golden color but get very... crunchy? They lose their marshmallow quality and have the texture almost resembling honeycomb. When I use storebought marshmallows, however, the marshmallows turn nice and golden and remain gooey inside, but I like the taste of homemade marshmallows better and prefer them. Is there a way to prevent them from going crunchy while baking but still have that golden color? The cookies are being baked at 350 for 11 minutes. The marshmallows have no egg or corn syrup.
This sounds like your marshmallows are fully caramelizing on top of the cookie.
I see two directions in which you could go.
The first, and probably easier, is to add the marshmallows later in the baking. With experimentation, you might be able to find out the exact time they need when they are already melted, but not yet caramelized. Hint: for this kind of experiment, you don't need to bake the whole cookies, you can try a series of baked marshmallows on a silicone mat, to systematically find your perfect baking time.
If this doesn't work out, then your marshmallows are unsuitable for melting. Then you are left with the second option, which is to try out different recipes, until you find one that melts well. Look for recipes with higher liquid content than your current one - but note that for any liquid that goes into the syrup part of the candy making process, it is not the initial amount that counts, but the final temperature at which you use it.