Abstract: High variability in soil and climatic conditions results in limited changes in soil aggregate–associated carbon (C) and nitrogen (N) levels as affected by management practices during a crop-growing season in the field. We evaluated the effects of crop species (spring wheat [Triticum aestivum L.], pea [Pisum sativum L.], and fallow), N fertilization rate (0.11 and 0.96 g N pot−1), and residue placement (no residue, surface placement, and incorporation into the soil) and rate (0, 20, and 40 g pot−1) on soil aggregation and C and N contents during a growing season under controlled soil and climatic conditions in the greenhouse. Soil samples collected from the field were grown with crops in the greenhouse and analyzed for aggregation and soil organic C, total N, particulate organic C, and particulate organic N contents in aggregates. Residue C and N losses, proportion of macroaggregates (>0.25 mm), and soil C and N contents in microaggregates (<0.25 mm) were higher in surface residue placement (20 g pot−1) under pea with 0.11 g N pot−1 than the other treatments. The soil organic C and soil total N were greater in surface residue placement (40 g pot−1) under wheat with 0.96 g N pot−1 in large and intermediate macroaggregates (8.00–4.75 and 4.75–2.00 mm, respectively), particulate organic N was greater in surface residue placement (20 g pot−1) under pea with 0.11 g N pot in large macroaggregates, but particulate organic C was greater in residue incorporation (20 g pot−1) under fallow with 0.96 g N pot−1 in intermediate macroaggregate than the other treatments. Under controlled soil and environmental conditions, soil C and N levels in aggregates changed rapidly during a crop-growing season. Surface residue placement increased soil aggregation and C and N storage with concurrent losses of residue C and N, but residue incorporation increased coarse organic matter fraction. Results from this short-term experiment in the greenhouse agree with those obtained from the long-term study in the field.