I see a lot of people asking for help managing their economy so I figured I'd create this guide with some of my thoughts. If you like this, I also wrote up a quickstart guide for your first 25 game years.
I believe there are two easy methods for conceptualizing how to manage your economy. You can think of your economy like a black box with inputs/outputs. Inputs are the base resources: food/minerals/energy. Outputs are things that drive your empire forward: research/unity/ships (alloys). You can either look at improving your inputs and figure out how to spend them to produce outputs (bottom-up approach) or you can look at your outputs and pick one to improve production of somehow (Top-down approach).
In the early game, you are usually in bottom-up mode. You look for planets/systems with good raw resource production and spend whatever excess you have on outputs. You look at whichever raw resource income is the worst and work on fixing that by building districts/stations to harvest it. Occasionally when you have excess of something you build a building that consumes it to get rid of the excess. This is fine, but you are basically just moving from solving one crisis to the next as your economy shifts from producing an excess/deficit of one raw resource to the next. You are cramming as many inputs as you can into the black box and hoping it produces some useful outputs.
This isn't a bad way to play, but it lacks planning and efficiency. You are living in the now rather than planning for the future.
At some point after the early game, you need to shift to the Top-down approach. This is where you pick some output of your empire (research/unity/alloys) and work on supporting and improving it. For example, lets say you have the option to upgrade a research lab. Before you do this, you need to ensure that you can actually support it. Do you have enough food to feed the lab technicians? Can you support the increased consumer goods needs? Do you have enough income of the required strategic resource to spare? Do you have new pops to work these jobs or will your farmers promote themselves and cause starvation?
These problems must be fixed before you even think about upgrading the building. You need to try and visualize how this upgrade will effect your current economy and have a good idea what it will cost you. If you just upgrade and build with no consideration for the effects (upkeep/pop promotion/trade-offs) then your economy will spiral into chaos. Your desired outputs require certain inputs.
Admittedly, this approach is more difficult. It requires more game knowledge and future planning to pull off, but the more you play, the more you should find yourself using the top down approach instead of bottom up.
You can plan things all you want, but sometimes shit happens that throws everything into turmoil. It could be a weird event, marauders, a crisis, or a war declaration by another empire. There are some things you just can't predict. If you find yourself with multiple negative incomes and rapidly declining stockpiles, you need to go into damage control mode. Your economy has sprung a leak and needs to be fixed. How do we fix leaks? We shut off some valves. In this case, we need to shut off the output valves (research/unity/alloys).
Start by disabling buildings that consume the resources you are running out of (or de-prioritize the jobs). For example, if you are running out of consumer goods, shut down research labs. If you are running out of minerals, shut down alloy foundries (NOT civilian industries, unless you also have excess consumer goods to handle the shutdown). If you are running out of energy, sell resources you have excess of, starting with alloys and excess strategic resources (worth the most and not needed to keep your economy afloat). If possible, pause the game while you do this (keep in mind the monthly numbers won't update until the next month). Avoid shutting down things that increase happiness/amenities/reduce crime (unless you have a lot of excess). Unhappy pops produce less which can cause you to spiral out of control.
Once you have stopped the leak, you need to work on plugging it. Improve the production of whatever resources you lack by shifting pop jobs or creating new jobs (thru districts/buildings) that produce what you need. Also be careful not to construct anything that will cause further drain on that resource. Once the crisis is averted you can shift back to top-down/bottom-up management.
© Post "Economy Management Guide" for game Stellaris.
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