Yes, yogurt should generally be stirred before storing in containers to ensure even distribution of cultures and prevent separation, resulting in a consistent texture and flavor throughout.
When yogurt sits, especially after being freshly made or purchased in a large container, it tends to separate. This separation results in a layer of whey (a watery liquid) forming on top and a thicker, more solid layer at the bottom. Stirring the yogurt before portioning it into smaller containers helps to redistribute the whey and solids evenly. This ensures that each serving you take from the smaller containers will have the same creamy texture and tangy flavor. Without stirring, the first few servings might be overly watery, while the last few could be excessively thick. Stirring also helps to maintain the consistency of the live and active cultures throughout the yogurt, which are beneficial for gut health. A gentle stir is all that's needed; avoid vigorous mixing, which can break down the yogurt's structure and make it thinner.
If you're transferring yogurt from a large container to smaller ones for individual servings, use a clean utensil to avoid introducing bacteria that could spoil the yogurt prematurely.