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Scattering by atmospheric turbulence is one of the main challenges in creating long free-space optical links, and specifically links of entangled photons. Classical compensation methods are hard to apply to entangled photons, due to inherently low signal to noise ratios and the fragility of entanglement. We have recently shown that we can use the bright laser beam that pumps spontaneous parametric down conversion to control the spatial correlations between entangled photons for compensating their scattering. In this work, we apply the pump-shaping technique to compensate for scrambling of correlations between entangled photons that scatter by emulated atmospheric turbulence. We use a spatial light modulator and Kolmogorov's turbulence model to emulate atmospheric turbulence in the lab, and enhance the entangled photons' signal by a factor of fifteen using pump optimization. We show this for both static and dynamic emulated atmosphere, and demonstrate also the compensation of the scattering of a higher-order mode. Our results can open the door towards realizing free-space quantum links with entangled photons, used in applications such as quantum key distribution.