Sustainable nitrogen (N) management in agroecosystems is crucial for supporting crop production and reducing deleterious N losses. Biochar application with N-fixing legumes offers promise for increasing soil N retention and input. Strategic, low application rates (112 kg ha−1) of pine and coconut feedstock biochars were tested in an established alfalfa (Medicago sativa) field. Soil inorganic N and plant growth, N concentrations, and δ15N were monitored over a growing season to follow mineral N availability, and plant N uptake and sourcing. Microbial and gene abundance and enzyme activity were measured to assess the potential for N cycling processes to occur. Biochar application had minimal effects on measured parameters. However, significant temporal dynamics in N cycling and correlations between alfalfa δ15N and soil N availability indicate differing plant N sourcing over time. Our findings indicate that low application rates of biochar in established alfalfa fields do not significantly affect N cycling, and that managing alfalfa to maximize N fixation, for example by intercropping, may be a better solution to increase N stocks and retention in this system. To determine when biochar can be beneficial for alfalfa N cycling, we need additional research to assess various economically-feasible biochar application rates at different alfalfa growth stages.