If a bakery primarily sells its food directly to consumers, but 40% of its annual sales are to wholesale facilities, does the bakery have to register?

No. The bakery is a “retail food establishment” and does not need to register. A retail food
establishment is exempt from registration if the annual monetary value of sales of food products
directly to consumers exceeds the annual monetary value of sales of food products to all other
buyers (21 CFR 1.226(c) and 1.227).