Joost Bakker has had a gutful. Standing in trademark T-shirt and jeans in front of a red For Sale board, the florist and sustainability crusader has pulled the pin on plans to build experimental off-grid residences on the vacant lot behind him, in the township of Kallista, an hour's drive from Melbourne.

As Bakker sees it, he has been brought undone, after almost two years' wrangling with the local Yarra Ranges Shire Council, by bureaucratic red tape, ongoing delays and costly changes. "I don't think I'll get over it for a while when you put that much time and energy into it," he says. "I had such dreams for this site. It was going to be the next 20 years making this a reality."

His mood is an about-face to a similar autumn day a year ago – bleak skies, a bit nippy, leaves on the turn – when an upbeat Bakker stood on the same spot outlining those ambitious dreams for the site he has now put on the market.

On the decontaminated land, where a Caltex service station operated a decade earlier, Bakker sketched his vision for a series of multi-level modular residences ("future caves") he'd designed, which included a fish-filled aquaponic system and worm farm converting organic waste into nutrient-enriched soil for green roofs growing organic food.

Talented Oakridge Wines husband-and-wife chef team Matt Stone and Jo Barrett were to live in and off the self-sustaining structure for a year – to be filmed for a documentary – to prove they could use the house to create a nourishing, waste-free diet from what they cultivated.

More importantly, the project – given the title New Holland – goes to the heart of whom Bakker is. The eco-warrior has long held the idea of transforming the rooftops of our cities and suburbs into productive urban farms.

Our food system is the primary cause of pollution, wilderness destruction and, worst of all, supplies food that's making us sick.

From a young age, Bakker – who migrated to Australia with his parents Joop and Lia and three brothers in 1982, aged nine – recalls being fascinated by the environment and wastefulness.

Growing up on the family's flower farm, he was struck by the inefficient and unproductive way houses were designed. "I was 12 or 13 when I started thinking this way, how stupid (our houses) are," remembers Bakker.

It was this thinking, too, that spurred Bakker as a young florist starting out to incorporate a mix of upcycled materials and found objects into the amazing floral installations he created for Melbourne restaurants such as Attica, Rockpool and Stokehouse.

It became the catalyst for some of Bakker's very public, high-profiled waste-free restaurant projects, too. It began a decade ago with Greenhouse by Joost, a three-month pop-up, made from recycled and recyclable materials, in Melbourne's Federation Square, which featured a rooftop garden supplying the restaurant.

Other Greenhouses followed in Perth (2009) and Sydney (2011), before popping up again in Melbourne for the 2012 Food and Wine Festival. This prompted Bakker to launch Australia's first waste-free restaurant, Silo, which composted anything left over. He then turned the place into a soup canteen, called Brothl, which used bones and leftovers from other restaurants to make broth.

"It was about looking at the infrastructure in our buildings as a way for us to source our food," says Bakker. He credits his Dutch heritage for the way he sees the world, although he spurned it during his early years in Australia to assimilate. His homeland has long relied on a controlled environment – a system of artificial levees – to prevent it from being flooded. "Holland has had a big influence on the way I think and my work," he says.

Certainly some of Bakker's success with his projects stems from a creative streak and keen eye for design – there's an artistic sensibility and simple beauty about his work. It's not only in his floristry or biophilic structures, like Greenhouse, and his own home at Monbulk, where he lives with his wife and two daughters. For the past few years, his Birdcage marquee for Lexus at Flemington Racecourse during the Melbourne Cup Carnival has been wowing race-goers.

"If I had stayed in Holland, I think I would have ended up in a creative school, studying arts," says Bakker. "I would have been an artist." For a short while, he entertained the idea. He even had a couple of exhibitions in the early 2000s.

Unsurprisingly, Bakker still cherishes fond memories of his mother taking him as a six-year-old to have lessons with a local artist. "All I wanted to do was draw," Bakker remembers. "He taught me how to draw, made me see light, texture, shadows, landscapes." His mother, who liked to paint and sketch in her spare time, also escorted a young Bakker to galleries and second-hand shops, where his appreciation for art and recycling grew.

It was in Australia, though, that Bakker learned to appreciate the land and what we do with it. Even as a schoolboy, he loved watching his father and brothers working the farm. "I felt like I was part of it," Bakker says. "I loved helping. I had my work clothes in my school bag."

Now, it's still what we're doing to the land that is his focus, but not always in a good way. Bakker is a big believer that the lack of beneficial bacteria in our diet – due to the absence of earthworms enriching the soil our food is grown in – is causing a range of maladies, including depression and anxiety. "Our food system is the primary cause of pollution, wilderness destruction and, worst of all, supplies food that's making us sick."

That's what makes the Kallista decision so hard, because he saw his project as an antidote. His decision also triggered a rare outburst from a frustrated Bakker on social media with a flurry of frank Instagram posts detailing just six of 18 projects that had failed to launch in the past decade – ones he was convinced would really happen.

In addition to New Holland, there was a rooftop farm atop National Australia Bank's Melbourne headquarters, the London edition of Greenhouse, a radical building designed to upcycle waste at Eastland Shopping Centre, an edible hanging garden on Sydney's Pyrmont Bridge using soil from surrounding restaurants' composted organic waste, and a glass waste recycling plant at Queen Victoria Market.

"I didn't know how stressed I was until I pulled the pin," says Bakker over kitchen-garden soup at his home in Monbulk. "I get fixated on trying to achieve something. I don't see the s---."

Bakker's social media flare-up triggered thousands of "likes" and hundreds of comments. "I was humbled and shocked by the reaction," he admits. "I'm surprised in a way there's that much support and that many people following and excited by the concepts, so that has really blown my mind."

More than just a cathartic experience, Bakker is now harnessing the positive feedback. Suddenly unburdened of Kallista, Bakker is using his free time and energy to refocus on floristry. He has planted flowering eucalypts, maples and peonies, among others, adding to the 300-plus varietals he already has, to complete "the most amazing garden" he imagined when he bought the block 15 years ago.

To a degree, it's in his blood. While his father cultivated flowers and bulbs, his grandfather was a florist. And Bakker acknowledges that flowers, amid his sometimes wild and hectic life, remain his one constant. "Every week, I leave at 4am to get into the city early with my flowers. By 1, I'm finished."

Bakker is also helping to ramp up the fight to have the sale of raw milk legalised. He believes raw milk, like bacteria-enriched soil, contains good bacteria addressing such health issues as allergies, asthma, autism and gut immunity.

"It's the fastest-growing agricultural business in Europe and the United States," he says. "It's sustainable, doesn't need subsidies, there's a huge market for it and people are demanding it."

Bakker says the Australian Raw Milk Movement, established by a volunteer group of consumers and producers, is preparing a comprehensive legislative framework, based on overseas platforms, to allow the sale of raw milk. "Here's a model [that's] highly regulated, safe and offers relief to thousands of small-scale farmers struggling and losing money."

Despite feeling "bloody frustrated" by the Kallista setback, Bakker remains confident he can establish a similar closed-loop symbiotic building somewhere else. He doesn't rule out overseas as an option. "At the moment, I am working on some alternative ways to realise a prototype," he says. "I just have to get it up."

And if these projects weren't enough, Bakker is helping to set up an urban farm and restaurant, promoting sustainable design, recycling and zero waste, on the rooftop of the proposed Brickworks shopping centre development in Burwood.

"I feel like the past 25 years have been my apprenticeship and now I just want to get on with executing ideas," he says.

"I have no doubt if we show the world we can grow a lot of beautiful food … and prove on top of that it's much more nutrient-dense than we currently eat and provides us with all the elements we need to help us live healthy lives, I think that's a game changer."