Cut only the florets off the broccoli and place them in a food processor that is fitted with the multi-purpose blade. Pulse until you have broccoli confetti, you need two cups in total). Alternatively, you can chop it by hand until you have very fine broccoli.
Whisk the flour, sugar, baking powder, salt, thyme, onion powder and baking soda together. Stir in the broccoli and one cup cheddar cheese.
In another bowl whisk together the yogurt, eggs and canola oil. Pour the wet ingredients into the dry and stir until you have a thick and moist dough.
Spray two 12 cup muffin tins with non-stick spray.
For a cream cheese centre, add a generous tablespoon amount of batter to 18 muffin cups, add a teaspoon of cream cheese and top with another generous tablespoon of batter. If opting out of the cream cheese, distribute the batter evenly between 18 muffin cups. Top each muffin with the remaining 1/2 cup cheese.
Cook 18 minutes. Remove from oven and brush red pepper jelly over each muffin and return to oven for another two minutes. Remove and allow muffins to cool completely.
Trace a butter knife gently around each muffin to release and cheesy bits. Remove from pan and store in an airtight container.