We report on the inscription of optical waveguides into crystalline bismuth germanate (Bi4Ge3O12, BGO) via the femtosecond laser direct-write (FLDW) technique. We found that by utilizing femtosecond laser pulses at Megahertz (MHz) repetition rates, a uniquely different fabrication regime can be exploited. In this paper, we show that cumulative heating effects can initiate a local transformation of the crystalline structure into an amorphous (glass-like) state that is characterized by an increased refractive index. We compare and contrast this novel, type-I modification based waveguide inscription regime with the previously reported fabrication of type-II damage/stress field structures in BGO and present measurements that indicate that the femtosecond laser writing process unavoidably causes a reduction in the electro-optic coefficient in the waveguides as compared to the bulk material. We discuss the potential of this technique for the fabrication of advanced sensor arrays for high-energy radiation detection and voltage sensing applications.