Xylulose and ribulose are rare keto-pentoses which are in high demand for the synthesis of commodities and fine chemicals. The production of keto-pentoses via isomerization of aldo-pentoses presents a carbon-efficient synthetic method. However, the isomerizations are equilibrium processes with thermodynamically limited yields of the products. In this work we examined isomerization of aldo-pentoses into keto-pentoses in the presence of NaH₂PO₄ + Na₂HPO₄ as a soluble catalyst at pH 7.5. A reaction network was proposed based on product distribution with D-(1-¹³C)-ribose as a substrate. Additionally, kinetics of the isomerization reactions was addressed. Selectivity for the keto-pentoses dramatically depends on the structure of the substrate. Arabinose and xylose give rise to a number of isomeric pentoses with low selectivities for the target products. Investigation of the reaction kinetics suggests that xylose and arabinose slowly isomerize into xylulose and ribulose, respectively. The latter react further significantly quicker to produce a number of isomers as subsequent products. This causes a complex mixture of products with low selectivity for the keto-pentoses. In contrast, ribose and lyxose as substrates yield ribulose and xylulose with rather high selectivities of 68–79% at 20% conversion. Ribose and lyxose quickly isomerize into ribulose and xylulose, respectively, whereas the subsequent processes are relatively slow. This results in a high selectivity for the keto-pentoses based on ribose and lyxose. Moreover, the isolation of xylulose from the reaction mixture was also studied. Xylulose can be selectively recovered after the isomerization of lyxose using anionic extraction with o-hydroxymethyl phenylboronic acid (HMPBA). After extraction, the aqueous phase containing phosphates and remaining lyxose can be recycled. After four cycles, the yield of xylulose reached 37% though only 19% can be achieved under batch conditions. Xylulose can be further recovered from the organic phase by back extraction using an acidified solution. Ribulose can also be extracted as an anionic complex with HMPBA, though ribose is co-extracted in this case and a separation of ribulose from ribose cannot be achieved. Extraction of the keto-pentoses occurs due to formation of β-xylulose–HMPBA and α-ribulose–HMPBA anionic complexes, whose molecular structures were established by NMR and MS.