The Breeding Bird Survey (BBS) provides the best data on Lincoln's Sparrow population trends in Canada, although it provides limited coverage of the northern boreal and subarctic where much of the population breeds; for this reason confidence in the national trend is only medium. The long-term trend shows a substantial population increase from the 1970s to the mid-1980s, followed by some minor fluctuations around a gradual decline, but with current abundance still 65% higher than in the early 1970s. Regional trends largely reflect the initial increase, but otherwise are quite variable. In British Columbia and the Prairie provinces, populations remain at elevated levels, whereas in eastern Canada there have been steady declines since the mid-1980s, resulting in overall large decreases relative to 1970 in central and southern Ontario and Quebec, and in the Maritimes.

The goal for Lincoln's Sparrow is to remain at or above its average population level from 1970 to 2022, based on the Breeding Bird Survey. Trend data show that Lincoln's Sparrow is currently within its goal range.