The alfalfa leafcutting bee, Megachile rotundata F., is used extensively to pollinate alfalfa for seed production in western North America. However, it usually is not possible to sustain bee populations in the United States. In the managed pollination system, variable microenvironments are experienced by developing M. rotundata during the nesting season that may influence bee reproductive success. In this study, bee cells were produced in a small alfalfa field and collected from domiciles according to nesting boards and different portions of boards. Examination of cells showed that the production of live overwintering prepupae, diseased larvae, other dead eggs and larvae, and cells attacked by natural enemies varied according to board orientations and positions, and portions of the boards. Northeast-facing board samples were significantly heavier and had more pollen balls and chalkbrood compared with southwest-facing boards. Lower boards in stacks had significantly more chalkbrood than upper boards. Outer portions of boards had significantly more live prepupae and less chalkbrood than middle and inner portions, and outer and middle portions had less summer-emerging bees. These results suggest that reproductive success could be altered by changing the orientation of boards within domiciles or changing the designs of domiciles. To accurately assess the quality of bee populations managed in the commercial loose cell system, a sample of bees should be taken from a pooled sample from all boards in each domicile. Each domicile sample should then be evaluated according to its proportional contribution to the whole field's progeny production (e.g., by weight or volume).