We have solutions to this for most (maybe all) contexts, at least as far as agriculture is concerned, in regenerative agriculture[0]. It requires a paradigm shift from the dominant type of agriculture taking place in the US and many other parts of the world, but it is not only better for soils and ecosystems – it's probably much better for our health as consumers, potentially more profitable for farmers, and can have an enormous positive impact in reigning in climate change.
It can seem too good to be true, but consider that when we mess with one aspect of nature by say, growing mono-culture crops rather than poly-cultures, we end up needing to intervene in many other aspects of ecosystems. The choice to annually till fields and grow acres upon acres of single crops year after year means we also need to recreate (poorly) natural systems of fertility (fertilizers), competition defense (herbicides), pest defense (pesticides), and disease defense (fungicides).
This model has other negative externalities as well, such as soil erosion, poor natural water infiltration and holding capacity, leaching of fertilizers and *-icides into surrounding areas and bodies of water which interrupt natural processes and are detrimental to life and health elsewhere, poor carbon sequestration, etc, etc.
The core principles of regenerative agriculture are to mimic nature and take advantage of natural processes rather than fighting them at every step, and to avoid intervening whenever possible. In the same way that the fastest and most maintainable line of code is the one you don't have to write, the cheapest and most effective agricultural practice is the one you don't need to do.
For those interested in a deep dive with a farmer from North Dakota who is very successfully putting these ideas into practice, see Gabe Brown[1] (who I first heard about here on HN, and for which I'm very grateful). If you're interested in agriculture, farming or even just gardening, I highly recommend watching the whole video. For a higher level and more accessible take, check out the documentary Kiss the Ground[2].
I've been trying to put these ideas into practice in my own ~100sq ft of growing space in NYC and, while it's still early in the growing season and hard to distinguish variables year-to-year, my garden is looking dramatically better this year[3] than at the same time in years past. Some of it for sure is a better sense of timing on my part and early warm weather here, but there are a lot of promising signs and I'm looking forward to seeing the state of things towards the end of the season when last year I had lost most of my tomato plants to pest pressures.
[0] https://en.wikipedia.org/wiki/Regenerative_agriculture
[1] https://www.youtube.com/watch?v=ExXwGkJ1oGI
[2] https://kisstheground.com/
[3] https://imgur.com/a/ybquJIX
Edit: The article specifically mentions regenerative agriculture, but says "pesticide companies know that these practices are often accompanied by increased pesticide use." I think it's a misnomer to call something regenerative agriculture when pesticide use is even higher than in conventional agriculture.