•We investigate online store choice decisions of multi-channel grocery shoppers.•We take traditional store choice drivers and multi-channel factors into account.•We allow their effect to change with growing online shopping experience.•At start, consumers tend to select the store of the preferred offline chain.•Online store comparison and the impact of online assortment increase over time. More and more grocery retailers are becoming multi-channel retailers, as they are opening an online alternative next to their traditional offline supermarkets. While the number of multi-channel grocery shoppers is also expanding at a fast growth rate, there are still large differences in online shopping frequency, and as a result, in the levels of experience with buying in the online grocery channel. This study wants to (i) identify the underlying drivers of online store choice and (ii) explore if and how these drivers change when multi-channel shoppers gain online grocery shopping experience. We investigate this question with an online store choice model using purchase data of an extensive UK household panel over a two-year period, covering all multi-channel retailers in the grocery market. Our results show that multi-channel shoppers, at the start of online grocery shopping, tend to select the online store belonging to the same chain as their preferred offline store, especially when the online store is strongly integrated with the offline store in terms of assortment. When online grocery shopping experience increases, multi-channel shoppers’ focus shifts from a comparison within a chain across channels to a comparison across chains within the online channel, resulting in an increasing importance of online assortment attractiveness and online loyalty when choosing an online store.