Greek yogurt acid whey, a dairy byproduct with limited utilizations, contains a large amount of lactose, which is recoverable by nanofiltration (NF). However, NF of acid whey is affected by challenges, particularly mineral scaling and membrane fouling. This study investigated the effect of heat-centrifugation pretreatment on the NF of Greek yogurt acid whey, at small pilot scale. Two NF membrane types (RL and DL) were compared, and RL was chosen due to its better permeability and more consistent performance. In the transmembrane pressure range between 15-30 bar, all NF runs exhibited quick initial flux reduction, due to membrane fouling. Operating at a transmembrane pressure of 25 bar gave the best combination of flux stability and separation efficiency, with a lactose rejection of around 99.7% and calcium rejection of 82-84%. At a transmembrane pressure of 30 bar, the lactose concentration factor increased, however fouling increased and calcium rejection fell to 78.8%. Hot centrifugation was used to remove calcium salts, in order to decrease fouling, but was not very efficient. Under crossflow conditions are more gradual decline in flux was obtained. Additionally, operating at 25 °C resulted in slightly higher flux than at 15 °C. Overall, moderate transmembrane pressure and crossflow increased process stability while achieving strong lactose retention. These results show that nanofiltration has the potential to be no-chemical-input method of recovering lactose from acid whey, facilitating the valorization of a challenging, yet abundant dairy byproduct.