In a medium saucepan, bring 2 3/4 cups water to a boil and stir in quinoa, salt, and pepper.
Cover and reduce heat to low, cook for about 20-25 minutes or until liquid is absorbed. Remove from heat and rest for 5 minutes. Fluff with a fork before placing in serving bowl and lightly cover to keep warm.
In the same pan you cooked the quinoa, heat extra virgin oil over medium-high heat. Add onions and cook until soft, about 5-8 minutes.
Stir in zest and juice and simmer for 1 minute. Note: I recommend starting with half the juice of a lemon and tasting first. I used the whole lemon, but I like it a bit tart. Also, be sure to zest the lemon prior to cutting and juicing.
Stir the onion mixture, parsley and quinoa together. Serve warm or at room temperature.