Two isogenic paired sets of alfalfa (Medicago sativa L.), a diploid (2n = 2x = 16) and tetraploid (2n = 32) set plus a tetraploid and octoploid (2n = 8x = 64) set, were compared in two growth chamber experiments for photosynthesis, N fixation, and dry matter accumulation on a whole‐plant basis. In Experiment A, each plant was harvested when it had open flowers on two racemes. Plants were harvested on a weekly basis in Experiment B.Within each set, the higher ploidy level reached the harvest stage approximately 9 days earlier. This maturity differential affected the comparisons of dry matter accumulation in Experiment A. Fresh and dry weights of leaves, stems, and roots did not differ in Experiment A. In Experiment B, the 4x had significantly greater herbage fresh weight than the 2x, while the 4x and 8x pair did not differ significantly. Net CO2 exchange (NCE) on a whole‐plant basis was equivalent across ploidy levels in both experiments. Acetylene reduction on both a whole‐plant and nodule‐weight basis and nodule number and nodule weight did not differ significantly at the different ploidy levels in either experiment. For measurements taken only during Experiment A, NCE was greater in the 4x compared to the 8x on a chlorophyll basis; transpiration was significantly greater in the 8x than in the 4x, and the chlorophyll a:b ratio was lower in the 8x than the 4x. Root respiration did not differ. When nonhomogeneous variances between ploidy levels were compared, in 17 out of 18 comparisons the lower ploidy level had the greater variance.The ploidy level had little effect on physiological processes in the isogenic populations of this study. Because greater variance exists with lower ploidy levels, selection should be more easily performed at lower ploidy levels.