If Transport Fever 3 achievements are not unlocking, the save almost always has a gameplay mod active or a gameplay setting changed from its default. The official manual says achievements are "generally unavailable if non-cosmetic mods are used or the gameplay settings are deviating from standard values." Start a new Free Game on a standard map with default gameplay settings and only cosmetic or Deluxe/Pre-Order content active, then earn an easy one such as Timekeeper (change the daytime) to confirm they count.
What switches achievements off?
Mods. Players found that the built-in Vehicles: No End Year mod disables achievements, and so does the official Trees from TF2 mod. The Deluxe Edition and Pre-Order content does not: players with both active still got achievements. A tidy rule of thumb from the forums: anything beyond the Deluxe and Pre-Order packs can block them, built-in mods included.
Gameplay settings. Any value changed away from its default in the Gameplay Settings tab counts as a non-standard game.
Custom maps. Many achievements specify Free Game, and players report they don't trigger on custom maps, including the maps that come with the Deluxe Edition.
Hushey walks through the new-game Mods tab and what each built-in mod does (from about 6 minutes in):
How do you fix it?
Check the save's mod list
Open Load Game, click the settings icon on the save's card, and look at its active mods. If the save allows editing, you can turn a gameplay mod off there. One player who thought they had no mods found Vehicles: No End Year switched on.
Check the gameplay settings
In the same place, check the Gameplay Settings tab for anything not at its default value.
Test with an easy achievement
Load the game and do something quick like changing the time of day (Timekeeper) or the weather (Weatherman). If the achievement pops, you're fine.
If the save can't be edited, or still doesn't count, start a new Free Game on a standard map with default settings. When a mod blocks achievements, the game shows a yellow notice about it on the new-game screen, so check for it before you click start.
Can you keep mods and still get achievements?
Community mods on mod.io such as Achievements Unbound say they let you keep earning achievements with other mods active. Enable it alongside your other mods when you create the game, or in the save's mod settings before loading. Players report it works on Steam for Windows, but its author says it does not fix achievements on custom maps.
Will achievements you already met unlock later?
There's no official word on retroactive unlocks. Assume an achievement you met in a blocked save will not unlock later; earn it again in a save where achievements are active.
The October 8 release (Version 40420) also fixed non-built-in mods activating themselves by mistake, so update before starting a fresh save.
For the full list of all 41 achievements and the campaign star goals, see Transport Fever 3 Achievements. To clean up mods, see Find and Uninstall Mods.