You may have missed the vegetarian items on the regular menus at some of the restaurants. For example, the Sci-Fi Dine-In serves seared marinated tofu and the Whispering Canyon Cafe offers veggie enchiladas as part of their standard offerings. In addition to these items, vegetarians can be accommodated at nearly every table service restaurant at Walt Disney World by special request.
When you're making your dining reservations, either online or via the 407-WDW-DINE phone number, simply note that their are vegetarians in your party. (You should do this at least 48 hours in advance.) If there are no appropriate items on the menu, then you will be offered substitutions. For example, often a main dish pasta can be made without a meat item or a vegetarian side dish or appetizer can be enlarged or enhanced to make it substantial enough for a main meal. In a situation like Mickey's Backyard BBQ, where all the main meals are meat-based, you will be offered an entirely separate vegetarian entree.
I have eaten at WDW restaurants with vegetarians a number of times and very often a chef will come out to the table to discuss food preferences and suggest some meal options.
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