The clean up, which will take place over the coming months, will transform station environments for customers.
All public areas are to be heavily cleaned, including platform furniture, signage, information boards, lighting, waiting shelters, overhanging vegetation, car parks, footbridges, station buildings and ingrained historic graffiti removal.
Where possible, ground in chewing gum will also be removed.
Phase one of the project will cost more than £100,000 and will run until April alongside a wider station audit to look at major improvements for the years ahead.
Director of Customer Experience Colin Lea said customers will notice a "dramatic difference" once the work was complete.
He said: "We want to transform the customer experience when using our services, but it will take time.
"We've got some fantastic stations, many with historic architecture, across our network - we want to look after that and place stations back as the heart of communities, becoming hubs for activity as well as gateways to the rail network.
"So getting them looking their best is our priority."
James Price, CEO of Transport for Wales added;
“It’s great to have started the deep clean of our stations across our network and the visual improvements will be seen by our customers.
This is the start of our plans at Transport for Wales and as we move forward, we will be investing £194 million in station improvements and building at least five new stations, as we continue our journey to positively transform rail services in Wales.”