You will find organic, or 'bio', products in almost every store and small organic shops in almost every neighbourhood. For example, the DM shops which carry small personal and household items have a good-sized and reasonably priced bio section. However, sometimes you need the bigger shops to find harder to get items.
Momo
The oldest organic market in the area also seems to carry one of the best selections. As an added bonus, there is a nice cafe which offers some vegan dishes as well.
Basic
The biggest and most comprehensive bio shop in the area. It is located next to the train and bus station in Bonn. Has a bakery.
Denns
Located just north of Bonn center, it is conveniently located across the street from a large parking garage where you can get one free hour validation. Has a bakery/cafe attached.
AlNatura
You can find produce and household items such as pull ups here in addition to the products you are used to seeing in other shops. It is also a payback partner.
There are 2 shops in the area, both with parking near-by. One is behind the Bonn train station. The other is across the river in Beuel.
Der Leyenhof
This is a local organic farm and shop. It's a fun place to visit with the kids as they have rabbits, pigs, chickens and goats. You can also get weekly deliveries of fruits and vegetables or anything else from their shop.
Bergfelds
This shop is located in Bad Godesburg on the pedestrian street and it has a surprisingly good selection for a small shop. Has a bakery.
Open Air Markets
There are open-air bio markets both in Bonn Center and Bad Godesburg.