There is no official Mycelarium best upgrade order, and the game does not publish one. What it does fix is the tree layout and the point prices on every node; what it leaves to you is the order. The order that actually works follows from one fact: food runs out, water does not.

Mycelarium best upgrade order: start from the resource that runs out

  1. Take the food-producing unlocks first. Food is the constraint on a run — salt rocks are finite, and a colony with no food left cannot grow at all.
  2. Take Water Efficiency once you can afford to skip it. Shots cost water every time you fire, so this node pays for itself immediately, but it does not unlock anything.
  3. Take the rest of HYPHAE as it becomes affordable. Shot Range and Shot Width change what each drag of the mouse produces, and Soil Penetration opens the harder soil.
  4. Then the ENZYMES line. Absorption and its descendants are long-term value, and Parasitism is what turns the trees above you into a resource.

Where food comes from and why it is the thing that stalls a run is in how to get more food.

What the tree does fix for you

The layout is the same for every run: Shot Range at the head of HYPHAE, Spore Mushroom at the head of FRUITING BODIES, Absorption at the head of ENZYMES, each with children you can only buy once the parent is paid for. The six attributes the game names as upgradeable are range, width, water efficiency, node cost, budding chance and soil penetration, and the printed prices tell you what a branch costs before you commit.

Every node and its price is listed out in the upgrade tree guide.

The constraint that decides when you can buy anything

Points are not the thing that stops you. They come from growing hyphae, and the same node keeps paying out while you keep shooting from it, so a colony with food will always have points to spend. What stops you is having nothing worth buying yet, which in practice means you are still short on the food-producing unlocks in FRUITING BODIES.

That changes once the renewable food source is running, because from then on points and food both accumulate and the rest of the tree is affordable in the order the layout suggests. Where those points come from is in the unlock points guide.