Unlike other crystals, the counter intuitive response of bismuth germanate crystals ($${\text {Bi}}_4{\text {Ge}}_3{\text {O}}_{12}$$
Bi
4
Ge
3
O
12
, BGO) to form localized high refractive index contrast waveguides upon ultrafast laser irradiation is explained for the first time. While the waveguide formation is a result of a stoichiometric reorganization of germanium and oxygen, the origin of positive index stems from the formation of highly polarisable non-bridging oxygen complexes. Micro-reflectivity measurements revealed a record-high positive refractive index contrast of $$4.25\times 10^{-2}$$
4.25
×
10
-
2
. The currently accepted view that index changes $$>1\times 10^{-2}$$
>
1
×
10
-
2
could be brought about only by engaging heavy metal elements is strongly challenged by this report. The combination of a nearly perfect step-index profile, record-high refractive index contrast, easily tunable waveguide dimensions, and the intrinsic high optical non-linearity, electro-optic activity and optical transparency up to $$5.5\,\upmu {\text {m}}$$
5.5
μ
m
of BGO make these waveguides a highly attractive platform for compact 3D integrated optics.