Diversification of conventional cereal-based cropping systems with pulse crops may aid producers to grow crops in an appropriate sequence and frequency with environmental, social, and economic benefits. This study examined the effects of including three pulse crops with different rooting depths (shallow- and deep-rooted) in wheat-based crop rotations on soil aggregate size distribution under semi-arid and rain-fed conditions. A 4 year cycle rotational study was established in Brooks, AB, using five selected treatments: continuous wheat, wheat alternately grown with lentil, field pea, or chickpea, or lentil and chickpea alternately grown with wheat. Soils were collected from 0–5 cm depth and dry-sieved to produce eight aggregate size classes, <0.053, 0.053–0.125, 0.125–0.149, 0.149–0.05, 0.05–1.0, 1.0–2.0, 2.0–6.35, and >6.35 mm. The continuous wheat treatment improved the macro-aggregates (>6.35 mm) development, whereas the rotations with pulse–wheat crops increased the micro- and meso-aggregates (0.50–1.0 and 0.15–0.5 mm) development. Soils sampled at 0–15 cm depth were used for soil organic matter and microbial analysis. The pulse–wheat rotations collectively had more light fraction organic matter (LFOM) than the continuous wheat, and chickpea alternated with wheat had the highest amount of LFOM in both years. All treatments had similar soil microbial biomass and microbial community composition. Our study underscores the contribution of pulse crops in cereal-based cropping systems in the formation of small aggregates.