Place almonds in a small ungreased frying pan. Toast over medium-low heat, shaking frequently until evenly browned and fragrant, 3 to 5 minutes. Remove from heat and let cool.

Place almonds in the food processor and chop coarsely. Remove and set aside.

Place edamame beans in the food processor and chop to a paste. Add basil, mint, garlic, and lemon zest; process until smooth while slowly adding in 1/2 cup olive oil. Add Parmesan cheese, salt, and almonds; pulse to combine. Stir in citric acid.

Transfer pesto to a jar with a tight-fitting lid. Pour a layer of olive oil over the top and cover with the lid. Refrigerate until serving.