Soil fertility decline is encountered in intensively managed low-residue systems. This long-term study (1998–2015) characterized soil organic matter (SOM) changes in the province of Prince Edward Island (PEI), Canada. The sampling locations were based on the 4 km × 4 km National Forest Inventory grid. Five subsamples were collected within a radius of 1–6 m from the centre location at the intersecting points on the grid and at locations 100 m in each cardinal direction covering the whole province every 3 yr, for a total of six cycles. The interpolation used the regression kriging method. Means ranged from 2.8% to 3.6%, coefficients of variation ranged from 0.22 to 0.28, and residual nugget and sill values were 0.03 and 0.06, respectively. From cycle 1 to cycle 6, acreage with 2%–3% SOM increased from 10% to 73% of the total area, acreage with 3.1%–4% SOM declined from 70.6% to 24% of the total area, and acreage with >4% SOM declined from 19% to 0.8% of the total area. Areas with a history of intensive agricultural activity were associated with the lowest SOM levels (2%–3%) at the beginning of the study, and SOM levels in those areas either remained unchanged or declined (<2%) at the end of the study, suggesting a predominance of recalcitrant SOM fractions with a longer turnover rate. This long-term study highlights the need to put in place strategies to increase levels of SOM to sustain PEI soil productivity.