The article presents the findings of a study investigating the effects of storing Jonagold apples for six weeks in a condition in which the vertical component of the geomagnetic field has been eliminated (near null GMF) and in control conditions representing those applied in traditional storage (i.e., in the local geomagnetic field (local GMF)). Analyses of the fruit were performed before the start of and three times during the experiment (i.e., following four, five and six weeks in storage). The contents of simple sugars were measured using the HPLC (high performance liquid chromatography) method; refractometry was applied to identify total extract; thermogravimetry was used to measure the water content, volatile substances and total ash; calorific value and intensity of respiration were examined by measuring CO2 emissions. Significant differences were found between the apples stored in the experimental and under control conditions, showing an advantage of storage in a condition with the vertical component of the geomagnetic field removed. Statistically significant differences were mainly identified in the speed of starch conversion into simple sugars, as well as the intensity of respiration and the appearance of the two groups of apples. Storage of fruit in a compensated geomagnetic field proved to be an effective method permitting an extended duration of storage without significant deterioration of the physicochemical and organoleptic properties of apples.