We derive flow equations for cold atomic gases with one macroscopically populated energy level. The generator is chosen such that the ground state decouples from all other states in the system as the renormalization group flow progresses. We propose a self-consistent truncation scheme for the flow equations at the level of three-body operators and show how they can be used to calculate the ground state energy of a general N-body system. Moreover, we provide a general method to estimate the truncation error in the calculated energies. Finally, we test our scheme by benchmarking to the exactly solvable Lieb–Liniger model and find good agreement for weak and moderate interaction strengths.