Given that rice husk biochar has been shown to modulate salinity in salt-affected acid soils, the objective of this study was to investigate the effects of organic amendment of salinized acid soils on P fractions, enzyme activities, and associated rice yield. Four treatments, viz. Rice–Rice–Rice, [RRR]; Fallow–Rice–Rice, [FRR]; Fallow–Rice–Rice + 3 Mg ha−1 of compost [FRR + Comp]; and Fallow–Rice–Rice + 10 Mg ha−1 of biochar [FRR + BC] were established at Ben Tre and Kien Giang sites, Viet Nam, over six consecutive crops. Soil properties at harvest of the sixth crop showed that there were diverse patterns of fractionation between P forms with respect to treatment. Overarchingly, biochar increased labile and moderately labile inorganic P and organic P by 30% to 70%, respectively, whilst compost had a relatively modest effect on these pools. Soil phosphatase activities at crop tillering increased following the FRR + Comp and FRR + BC treatments compared with those in RRR, except for acid phosphatase at Ben Tre. At harvest, there were no significant differences between the enzyme activities among the treatments. Rice yield was positively correlated with the more labile forms of P, soil C, and acid phosphatase activity. In the absence of organic amendments, there was no effect of triple versus double rice crops being grown in one-year cycle. Repeated application of biochar (10 Mg ha−1 × 5 times) showed potential to increase grain yields and total soil C in salt-affected acid soils, via modulation of P transformations to more plant-available forms.