Housing in metabolic cages for quantitative collection of urine and feces is necessary for nitrogen (N) metabolism studies but may have negative consequences for rat welfare. We hypothesized that providing shelters in metabolic cages would affect the rats’ behavior and reduce the precision of measuring N metabolism. Forty-eight growing male Sprague–Dawley rats were housed in metabolic cages for 9 d, constituting 4 d of adaptation and 5 d for quantitative measurement of feed intake and urine and feces excretion. Using a 2-factorial approach, half of the rats were fed a soybean meal diet, and the other half were fed a diet based on green protein (GP). Half of the rats in each dietary group were provided a ball-shaped shelter in their metabolic cage, and the other half had no shelter (n = 12 per treatment). Video recordings of rat location (cage floor, feed tube, or shelter) were performed on days −3 (adaptation period), 1, and 4 (collection period). Dry matter (DM) and nitrogen (N) digestibility were determined based on DM and N intake and fecal excretion. N metabolism was calculated based on additional measurements of urinary N excretion. The rats used the shelter primarily during the daytime and spent less time in the feed tube during the day than during the night (P = 0.0002). For rats without shelter, there was no difference between day and night in their presence in the feed tube (P = 0.94). The shelters did not interfere with measurements of feed intake, fecal DM, N excretion, or any of the derived N-metabolism-associated responses. There was also no significant effect on the variation associated with the estimated values, and no differences in contamination were detected visually or by rinsing the shelters. We conclude that using ball-shaped shelters to enrich metabolic cages is not a major risk of biocontamination and may improve the rats’ welfare.