Soil respiration (Rsoil) is one of the largest CO2 fluxes in the global carbon (C) cycle. Estimation of annual Rsoil requires extrapolation of survey measurements or gap filling of automated records to produce a complete time series. Although many gap filling methodologies have been employed, there is no standardized procedure for producing defensible estimates of annual Rsoil. Here, we test the reliability of nine different gap filling techniques by inserting artificial gaps into 20 automated Rsoil records and comparing gap filling Rsoil estimates of each technique to measured values. We show that although the most commonly used techniques do not, on average, produce large systematic biases, gap filling accuracy may be significantly improved through application of the most reliable methods. All methods performed best at lower gap fractions and had relatively high, systematic errors for simulated survey measurements. Overall, the most accurate technique estimated Rsoil based on the soil temperature dependence of Rsoil by assuming constant temperature sensitivity and linearly interpolating reference respiration (Rsoil at 10 °C) across gaps. The linear interpolation method was the second best-performing method. In contrast, estimating Rsoil based on a single annual Rsoil – Tsoil relationship, which is currently the most commonly used technique, was among the most poorly-performing methods. Thus, our analysis demonstrates that gap filling accuracy may be improved substantially without sacrificing computational simplicity. Improved and standardized techniques for estimation of annual Rsoil will be valuable for understanding the role of Rsoil in the global C cycle.