Whole Wheat Hogies

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Ive been working on a recipes for whole wheat hoagie rolls. Some days the hoagies turn out nice and fluffy but most days they flatten out. i dont know what to do?... the link to the recipe is below but i changed the bread flour to 2 cups and whole wheat flour to 2 cups. i also made it dairy free by using shortening instead of butter. when i make the normal recipe it turns out wonderful. HELP!!!

Link to the recipe is here http://www.thekitchenwhisperer.net/2012/07/02/super-soft-n-chewy-hoagie-rolls/ 

You're saying they rise just fine but fall when you put them in the oven? If that's the case then they may be overfermented. 

Because you added whole wheat to your recipe, it's possible that they are fermenting even more quickly than with white flour. So it's possible they are collapsing and not getting oven spring when you bake them. Try reducing the amount of time you let them rise right before putting them in the oven. Also watch the amount of time that it takes for them to complete the bulk fermentation (first rise). 

The other possibility is that because of the whole wheat, you're not developing enough dough strength. Try kneading the bread a little longer. 

Look forward to the photos. If you can, post one of the dough rolls before you put them in the oven, and then after.