In 1992, Rederiaktiebolaget Eckerö and Birka Line founded a jointly owned subsidiary, Eestin Linjat, to operate the MS Alandia on the fast-growing route between Helsinki and Tallinn.

The name of the company was reportedly selected for practical reasons as it required the change of only a few letters to re-paint Eckerölinjen into Eestin Linjat (or vice versa).

This was made worse after the Estonia-disaster in 1994 when many people in Finland began associating Eestin Linjat with EstLine, owners of the ill-fated MS Estonia.

In 1998 Eckerö Line acquired its first (and only) genuine cruiseferry, MS Nordlandia which replaced both of the previous ships sailing on the route.

In May 2004 Eckerö Line purchased the freight/passenger ferry MS Translandia as a second ship for the Helsinki–Tallinn route in response to the high demand for freight capacity after Estonia joined the European Union.