We develop a three-dimensional inversion code to image the resistivity distribution of the subsurface from frequency-domain controlled-source electromagnetic data. Controlled-source electromagnetic investigations play an important role in many different geophysical prospecting applications. To evaluate controlled-source electromagnetic data collected with complex measurement setups, advanced three-dimensional modelling and inversion tools are required.We adopt a preconditioned non-linear conjugate gradient algorithm to enable three-dimensional inversion of impedance tensor and vertical magnetic transfer function data produced by multiple sets of two independent active sources. Forward simulations are performed with a finite-element solver. Increased sensitivities at source locations can optionally be counteracted with a weighting function in the regularization term to reduce source-related anomalies in the resistivity model. We investigate the capabilities of the inversion code using one synthetic and one field example. The results demonstrate that we can produce reliable subsurface models, although data sets from single pairs of independent sources remain challenging.