Ultrafiltration (UF) can be used to concentrate yogurt to produce Greek-style yogurt (GSY) (UF-YOG), but this generates acid whey permeate, which is an environmental issue. However, when UF is applied before fermentation (UF-MILK), a nonacidified whey permeate is generated. For this study, two model GSYs (UF-YOG and UF-MILK) were produced to compare the composition, UF performance, and energy consumption of the two processes. For UF-MILK, skim milk was ultrafiltered with a 30 kDa spiral-wound UF membrane to achieve a 3× volume reduction factor (VRF). The retentate was fermented to a pH of 4.5. The UF-YOG process was the same except that regular yogurt was ultrafiltered. Both GSYs had similar protein (~10%) and solid content (~17%). As expected, lactic acid/lactate was not detected in UF-MILK permeate, while 7.3 g/kg was recovered from the UF-YOG permeate. Permeation flux values (11.6 to 13.3 L m−2 h−1) and total flux decline (47% to 50%) were constant during UF-MILK, whereas drastic decreases in these two membrane performance indicators (average flux: 38.5 to 10.9 L m−2 h−1; total flux decline: 2% to 38%) were calculated for UF-YOG. Moreover, for UF-YOG, UF membrane performance never recovered, even when drastic and repeated cleaning steps were applied. Energy consumption was 1.6 kWh/kg GSY and remained constant for UF-MILK, whereas it increased from 0.6 to 1.5 kWh/kg GSY for UF-YOG. Our results show that, although the composition of GSYs was similar for both processes, the UF step of yogurt concentration affected process efficiency due to drastic and permanent membrane fouling.