The INFLUX experiment has taken multiple approaches to estimate the carbon dioxide (CO 2 ) flux in a domain centered on the city of Indianapolis, Indiana. One approach, Hestia, uses a bottom-up technique relying on a mixture of activity data, fuel statistics, direct flux measurement and modeling algorithms. A second uses a Bayesian atmospheric inverse approach constrained by atmospheric CO 2 measurements and the Hestia emissions estimate as a prior CO 2 flux. The difference in the central estimate of the two approaches comes to 0.94 MtC (an 18.7% difference) over the eight-month period between September 1, 2012 and April 30, 2013, a statistically significant difference at the 2-sigma level. Here we explore possible explanations for this apparent discrepancy in an attempt to reconcile the flux estimates. We focus on two broad categories: 1) biases in the largest of bottom-up flux contributions and 2) missing CO 2 sources. Though there is some evidence for small biases in the Hestia fossil fuel carbon dioxide (FFCO 2 ) flux estimate as an explanation for the calculated difference, we find more support for missing CO 2 fluxes, with biological respiration the largest of these. Incorporation of these differences bring the Hestia bottom-up and the INFLUX inversion flux estimates into statistical agreement and are additionally consistent with wintertime measurements of atmospheric 14 CO 2 . We conclude that comparison of bottom-up and top-down approaches must consider all flux contributions and highlight the important contribution to urban carbon budgets of animal and biotic respiration. Incorporation of missing CO 2 fluxes reconciles the bottom-up and inverse-based approach in the INFLUX domain.