The abbey was founded as a daughter house of Kelso Abbey in the about 1191 (some sources say 1178) by David, Earl of Huntingdon, brother of William the Lion. The first abbot was Guido, Prior of Kelso, under whom the buildings were mosly completed. The church, dedicated to the Blessed Virgin and St. Andrew, was long, with transepts long. Edward I of England, John Balliol, David II, and James III were among the monarchs who visited Lindores at different times.
The abbey was sacked by a mob from Dundee in 1543, and again by John Knox and his supporters in 1559. In the following years the abbey buildings were quarried as a source of stone for buildings in Newburgh. All that remains of the abbey are: one of the gateways leading into the monastic enclosure; the groin-vaulted slype, leading from the cloister garth to the exterior of the Abbey; and parts of the chancel walls and western tower of the church, although the ground plan of the whole structure can still be traced.
Wooden panels of the early 16th century survive from the Abbey in the Laing Museum, Newburgh and, re-used in a Victorian cabinet, in St. Paul's Episcopal Cathedral, Dundee.