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A new and simple method for fabrication of nanofiber scaffolds with gradations in fiber organization is reported. The nanofiber organization, achieved by deposition of random fibers on the uniaxially aligned nanofiber mat in a gradient manner, directed morphological changes of applied adipose‐derived stem cells. These morphological changes and resultant biochemical changes can help mimic the structural orientation of complex biomechanical structures like the collagen fiber structure at the tendon‐to‐bone insertion site. In addition, chemical gradients can be established through nanoencapsulation in this novel scaffold allowing for enhanced biomedical applications.