The coupled-trajectory mixed quantum-classical method (CTMQC), derived from the exact factorization approach, has successfully predicted photo-chemical dynamics in a number of interesting molecules, capturing population transfer and decoherence from first principles. However, due to the approximations made, CTMQC does not guarantee energy conservation. We propose a modified algorithm, CTMQC-E, which redefines the integrated force in the coupled-trajectory term so to restore energy conservation, and demonstrate its accuracy on scattering in Tully's extended coupling region model and photoisomerization in a retinal chromophore model.