Why do fresh mandarin oranges get very bitter when baked?
What compound in mandarin oranges turns bitter when heated?
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The white, pithy part is a source of the bitterness. Either peel more thoroughly, or trim off with a knife.
The pulp of some oranges (of the navel variety), can turn bitter when exposed to air. http://www.preparedpantry.com/CitrusQuickGuide.htm