The elemental composition of single cells of Nitrosomonas europaea 19718 was studied via synchrotron X-ray fluorescence microscopy (XFM) as a function of inhibition by divalent copper (Cu(II)) and batch growth phase. Based on XFM, the intracellular Cu concentrations in exponential phase cultures of N. europaea exposed to Cu(II) were statistically higher than in stationary phase cultures at the 95% confidence interval (α = 0.05). However, the impact of Cu inferred from specific oxygen uptake rate (sOUR) measurements at the two physiological states was statistically not dissimilar at the Cu(II) doses tested, except at 1000 µM Cu(II), at which exponential phase cultures were significantly more inhibited. Furthermore, the elemental composition in uninhibited exponential and stationary phase N. europaea cultures was similar. Notably, the molar fractions of Cu and Fe, relative to other elements in N. europaea cultures were statistically higher than those recently reported in Pseudomonas fluorescens possibly owing to the preponderance of metal cofactor rich catalytic enzymes (such as ammonia monooxygenase) and electron transport mechanisms in N. europaea.