The PHO91 and PHO87 are parts of yeast's phosphate metabolism system. We investigated the influence of PHO91 deletion on the methanol utilization as a sole carbon source in Ogataea parapolymorpha through comparison of wet biomass, protein content, methanol oxidase (MOX) activity and acid-soluble and acid-insoluble inorganic polyphosphate (polyP) content, while growing on methanol and without any carbon source other than trace amounts from the yeast extract. The Δpho91 strain has a lack of wet biomass, protein content and MOX activity while grown on methanol (as a ΔMOX strain) and has the same numbers as a WT strain in media without methanol. We found two ways of recovering methanol utilizing capabilities for Δpho91 mutant—either adding MOX on plasmid under constitutive promoter control, or adding a Δpho87 mutation. Both Δpho91 + MOX and Δpho91Δpho87 strains showed all the parameters as a WT strain on methanol as a sole carbon source and without methanol addition. Further, we compare the polyP content of the strains in methanol media, media without a sole carbon source and media with glucose. All of the WT, Δpho91 + MOX and Δpho91Δpho87 strains, capable of utilizing methanol, have the P_i, acid-soluble and acid-insoluble polyP at the same levels with some variations. The ΔMOX and Δpho91 strains, despite both not being able to utilize methanol, showed very different levels of P_i and polyP’s, which can be interpreted as different mechanisms of the inner cell, leading to a loss of capability utilizing methanol in both of these strains.