In a large pot, toast quinoa over medium heat for 2-3 minutes.
Add oil, onion and pepper to the pot and saute over medium-high heat for 3-5 minutes, until soft. Add garlic, parsley, thyme and salt and cook 1 minute.
Stir in flour until combined (you don't want to see any white left - add gradually and if there's a little left over that's okay). Whisk in stock and then milk one cup at a time, whisking and waiting until the soup has thickened slightly before adding the next cup.
Bring to a simmer, stirring frequently. Reduce heat to medium (or medium-low) and cook uncovered for 15-20 minutes until quinoa is cooked, stirring often. Add corn and beans and heat through, serve.