A combination of good gardening techniques seem to work best for me.
On the fertilizer side/ certainly compost, but compost may consist, in part, of coffee grounds, shells, ash, and peels. In addition, grounds and pine needles are good for my acid loving blueberries, while peels and shells are good for tomatoes.
As far as pesticide alternatives/careful surveillance makes hand-picking pests early while they are still a small infestation possible, planting flowers and veggies that lure predators (or confuse pests) as well as some companion planting works well in my garden. Sprinkles of DE (diatomous earth) or BT gets rid of some pests, while home-made sprays (simple soap, garlic, hot pepper, tomato leaf), beer, and kaolin clay (fools and/or kills pests). Even growing sacrifice or trap-plants will work to lure pests away from favorites.
For anti-fungus spacing is important, but baking soda, oil, and water will help eliminate fungus on plants if used early and repeated often.
Of course, keeping the garden at its healthiest is important. Pests seem drawn to already stressed plants so a goodly supply of compost and enough mulch will prevent many problems before they start.
I'm sure I've forgotten some ideas at this obscene time of the day, but I am always on watch for garden problems and solutions. I look forward to getting more information.