The group is aiming to have around 400 hydrogen filling stations in the country over the next ten years.
The initial plan is to install 100 hydrogen stations in Germany over the next four years. The sites would be located in metropolitan areas, and each area would get ten refueling stations by 2023.
The objective of the plan is to deliver a refueling station at least every 90km of motorway between densely populated areas.
Linde chief executive officer Wolfgang Reitzle said that the company has been a pioneer in the further development of hydrogen technology for many years.
"Especially with respect to the series production of hydrogen refueling stations, we have achieved major advances over the last few years," Reitzle added
"The time is now right to roll out this environmentally friendly technology on a nationwide basis."
The group will invest around €350m ($500m) on this infrastructure project.
Besides this initiative, the latest agreement between partners includes the procurement and distribution of the necessary hydrogen and a request for support to the German federal government.
Shell Holding CEO Peter Blauwhoff said, "Following the foundation of the joint venture, Shell will play a significant role in the development of the future H2 retail station network in Germany."