The scheme is being run with returnables firm ClubZero. Customers will be able to opt in when placing an order, and then return their boxes via a drop-off point, or arrange for them to be collected via the ClubZero app.
Reusables are growing in popularity as a way to combat the issue, after years of focus on compostables and recycling. Before the 1950s, the idea of using a carton once and disposing of it was almost unheard of.
ClubZero says its products produce at least half the carbon footprint of single-use disposable packaging. Units are dropped off and picked up at the same time to save on trips, and cleaned with minimum water use.
Just Eat's Robin Cark said: "Building a more sustainable future for the food delivery industry is extremely important."
The takeaway giant, the largest food delivery service outside China, also recently launched eco-friendly seaweed-lined compostable packaging and sauce sachets.
Last month the Amsterdam-headquartered firm reported a €486 million first-half post-tax loss despite soaring sales amid heavy spending on marketing and expansion - including its well-known Euros ad campaign.
Marketing expenses increased by 204% to €295 million in the period, up from €97 million in the first half last year.
The six London restaurants taking part in the trial are:
Kin Cafe - Just Eat for Business
Kaleido - Just Eat for Business
Clean Kitchen Club
The Great Thai Restaurant
The Great Thai Grab & Go