Controlling multiferroic behavior in materials will enable the development of a wide variety of technological applications. However, the exact mechanisms driving multiferroic behavior are not well understood in most materials. Two such materials are the spinels MnV 2O4 and Mn3O4, where mechanical strain is thought to play a role in determining magnetic behavior. Bulk studies of MnV2O4 have yielded conflicting and inconclusive results, due in part to the presence of mesoscale magnetic inhomogeneity, which complicates the interpretation of bulk measurements. To study the sub-micron-scale magnetic properties of Mn-based spinel materials, we performed magnetic force microscopy (MFM) on MnV 2O4 samples subject to different levels of mechanical strain. We also used a crystal grain mapping technique to perform spatially registered MFM on Mn 3O4. These local investigations revealed 100-nm-scale "stripe" modulations in the magnetic structure of both materials. In MnV2O4, the magnetization of these stripes is estimated to be M z ~ 10 5 A/m, which is on the order of the saturation magnetization reported previously. Cooling in a strong magnetic field eliminated the stripe patterning only in the low-strain sample of MnV 2O4. The discovery of nanoscale magnetostructural inhomogeneity that is highly susceptible to magnetic field control in these materials necessitates both a revision of theoretical proposals and a reinterpretation of experimental data regarding the low-temperature phases and magnetic-field-tunable properties of these Mn-based spinels.