Season 1 was filmed entirely in Scotland
You can find places such as:

The Opening Scene - Inverness - Castle Leoch - The Gathering Village - Cranesmuir - Black Kirk -- Fort William - The Wedding Church - Sandringham House - The Witch Trial Palace - Lallybroch - Lallybroch Mill and St Anne's Abbey

Season 1

Season 2

The first part of season 2 was shot in Scotland, Prague, England and in the studio. The second part of the second season is again shot in Scotland.
There are the following places:
The port of Le Havre - The streets of Paris - Versailles, exterior and interior - Other places in Paris - the hospital of the angels.
Then in the second part:
The Old Fox's Lair - Prestonpans, the Tullibardine Chapel - The Duke of Sandringham estate and Culloden house

Season 3

The third season is unique in that the first 6 episodes are intertwined with two stories between 18th century Scotland and 20th century Boston in the United States.
However, all the American scenes were shot in Glasgow.For now, I will focus only on filming locations from the 18th century story.

Ardsmuir Prison - Helwater - Glasgow Printing House - Artemis Port of Embarkation - Silkies Island - Jamaica - Homecoming Beach - Governor's Palace, interior and exterior - The House of Geillis

Although throughout season 4, the Fraser family and their companions immigrated to the American colonies, notably North Carolina, filming took place entirely in Scotland.

Cemetery where Hayes was buried - River Run - Governor Tryon's residence - The forest where Claire strays - The Indian camp - Another part of the forest, further inland and finally, Fraser's ridge.

Season 4

Season 5

The fifth season was filmed in Scotland, primarily at Wardpark Studios in Cumbernaud near Glasgow. Over the years, the series has built up an impressive base, with huge sets and a vast warehouse for costumes and props.

Wardpark Studios - The Big House - The Regulators' Camp - The North Carolina Forest - Steven Bonnet's Fight Scene Building - Brianna's Abduction and Rescue Beach and 1960s locations