Long-term use of soil, crop and fertilizer management practices alters some soil properties, but the magnitude of change depends on soil type and climatic conditions. A field experiment with a barley (Hordeum vulgare L.)–wheat (Triticum aestivum L.)–canola (Brassica napus L.) rotation was conducted on a Gray Luvisol (Typic Cryoboralf) loam soil at Breton, Alberta, Canada. Effects of 19 or 27 years (from 1980 to 1998 or 2006 growing seasons) of tillage (zero tillage [ZT] and conventional tillage [CT]), straw management (straw removed [SRem] and straw retained [SRet]) and N fertilizer rate (0, 50 and 100 kg N ha−1 in SRet, and 0 kg N ha−1 in SRem plots) were determined on total organic C (TOC) and N (TON), light fraction organic C (LFOC) and N (LFON), macro organic matter C (MOM-C) and N (MOM-N), microbial biomass C (MB-C), and mineralizable C (Cmin) and N (Nmin) in the 0–7.5 and 7.5–15 cm or 0–5, 5–10 and 10–15 cm soil layers. Zero tillage and SRet tended to have higher, and N fertilizer treatment usually had higher mass of TOC, TON, LFOC, LFON, Cmin and Nmin in soil compared to the corresponding CT, SRem and zero-N control treatments, especially in the surface soil layers. Soil MB-C, MOM-C and MOM-N in soil generally tended to be higher with SRet than SRem, and also with N fertilizer than zero-N. There was no additional beneficial effect of ZT in increasing MB-C in soil. There were close and significant correlations among most soil organic C or N fractions, except for MB-C which did not correlate with MOM-N, and Nmin did not correlate with MOM-C. Linear regressions between crop residue C input and soil organic C or N were significant in most cases, except for MB-C and Nmin. Compared to the 1979 data, all treatments that did not receive N fertilizer (CTSRem0, CTSRet0, ZTSRem0 and ZTSRet0) showed a decrease in TOC concentration in the 0–15 cm soil layer over time, with the highest decrease in the CTSRem0 treatment. Straw retention and N fertilizer application at 50 and 100 kg N ha−1 under both ZT (ZTSRet50 and ZTSRet100) and CT (CTSRet50 and CTSRet100) resulted in a strongest increase in TOC during the first 11 years, and since then the TOC decreased under both N rates but 50 kg N ha−1 rate under CT (CTSRet50) showed the strongest negative effect on TOC in soil. In conclusion, elimination of tillage, straw retention and N application all improved organic C and N in soil, and generally differences were more pronounced for light fraction organic C and N, and between the most extreme treatments (CTSRem0 vs. ZTSRet100) for each dynamic organic fraction. This may be better for the long-term sustainability of soil quality and productivity.