A comet flyby, like the one planned for ESA’s Comet Interceptor mission, places stringent requirements on spacecraft resources. To plan the time line of in situ plasma and neutral gas observations during the flyby, the size of the comet magnetosphere and neutral coma must be estimated well. For given solar irradiance and solar wind conditions, comet composition, and neutral gas expansion speed, the size of gas coma and magnetosphere during the flyby can be estimated from the gas production rate and the flyby geometry. Combined with flyby velocity, the time spent in these regions can be inferred and a data acquisition plan can be elaborated for each instrument, compatible with the limited data storage capacity. The sizes of magnetosphere and gas coma are found from a statistical analysis based on the probability distributions of gas production rate, flyby velocity, and solar wind conditions. The size of the magnetosphere as measured by bow shock standoff distance is 105–106 km near 1au in the unlikely case of a Halley-type target comet, down to a nonexistent bow shock for targets with low activity. This translates into durations up to 103–104 seconds. These estimates can be narrowed down when a target is identified far from the Sun, and even more so as its activity can be predicted more reliably closer to the Sun. Plasma and neutral gas instruments on the Comet Interceptor main spacecraft can monitor the entire flyby by using an adaptive data acquisition strategy in the context of a record-and-playback scenario. For probes released from the main spacecraft, the inter-satellite communication link limits the data return. For a slow flyby of an active comet, the probes may not yet be released during the inbound bow shock crossing.