Nano-/micro-scale α and β NaYF₄:Er³⁺,Yb³⁺ crystals with ultra-efficient upconversion (UC) of near infrared (NIR)-to-visible (VIS) light were prepared by annealing following citrate-assisted hydrothermal synthesis at 200 °C. Excess fluoride ([F]/[Y + Er + Yb] molar ratio = 9) helped promote the formation of the hexagonal β phase while simultaneous addition of citrate led to crystal shape and size control. The citrate caused the morphology of the β phase crystals to change from irregular elongated microtubes to hexagonal prisms, with particle size decreasing with increasing citrate concentration. However the presence of citrate led to significant deterioration of the upconversion luminescence of the β NaYF₄:Er³⁺,Yb³⁺ crystals due to surface quenching by adsorbed citrate moieties. We have found that annealing at 700 °C restored the NIR-to-VIS upconversion luminescence (predominantly green) of the citrate-modified β NaYF₄:Er³⁺,Yb³⁺ crystals and also led to a dramatic enhancement (over several orders of magnitude) not previously reported. According to Raman spectroscopic evidence, annealing led to improved upconversion efficiency via elimination of internal defects and surface hydroxyl/citrate groups. Further, we report on the preparation of unexpectedly strong upconverting (predominantly red) α cubic phase NaYF₄:Er³⁺,Yb³⁺ nanocrystals.