Research has shown significant effects of timber harvest residue management on soil organic carbon (SOC), but less impact has been observed on the available P pool. The objectives of this study were: (1) to estimate the effects of different timber harvest intensities and P fertilization on soil labile P and P fate over time; and (2) to identify which soil P fractions supply P to Eucalyptus plantations cultivated in soils with low P availability. P fractions were assessed using Hedley’s sequential extraction methodology, which corresponds to differing degrees of soil P lability. Three timber harvest intensities (stemwood only, whole tree and whole tree plus litter) and two levels of P fertilization (0 and 44 kg ha−1 of P) were used. A total of 70% of total soil P was found in a non-labile form in the whole tree plus litter removal treatment, while in the whole tree treatment only 66% was found in this form. Removal of harvesting and litter residues resulted in a 40% reduction in the labile P fraction when compared to stemwood only harvested treatment even with fertilizer application. Acid phosphatase activity, which is crucial in mobilizing P for plant uptake, was 45% higher in soils that did not receive P fertilizer, but it did not resulted in higher concentration of labile P. Timber harvest intensity and P fertilizer application did not influence the soil total P concentration over 12 years of Eucalyptus cultivation. However, there was an increase in non-labile and inorganic P fractions and a reduction of labile and organic P fractions with increasing timber harvest intensity. The organic, moderately labile P fraction was the main source of P to the trees under low P availability conditions. Acid phosphatase and low molecular weight organic acid excretion seem to be important strategies of Eucalyptus species to improve P uptake.