Resources can be manually collected from each building type. You can build Farms, Sawmills, Quarries, and Mines to collect each resource type. Farms produce food, Sawmills produce lumber, Quarries produce stone, and Mines produce Iron. Once your resource production reaches 100%, you can start collecting your desired resource! Upgrade your resource buildings to increase the capacity of each resource. Remember, production speeds over time, the longer it goes, the faster it grows!
Another way to increase your resource production is to take over wildernesses around you! Go to the Map View and click on the Woods, Hills, etc. around your City to learn more. Lower level Wildernesses have fewer protectors, and require you to send fewer Troops when you attack.