Current interest in boron incorporation into carbonates arises from the observation that the isotopic composition of carbonates depends on the pH of the fluid from which they precipitated. This finding opened the possibility of using boron isotopic composition of natural carbonates as a paleo-pH proxy. In this study, coprecipitation of boron by calcite was investigated using Atomic Force Microscopy (AFM), as a function of pH, supersaturation and boron concentration. In situ AFM observations reported here provide experimental evidence of boron incorporation into calcite, which takes place to a greater extent at high pH (9.5) and under close to equilibrium conditions. Moreover, we report nanoscale observations that give indirect evidence of the incorporation of boron in non-lattice sites. Step-specific interactions of tetrahedrally-coordinated boron with calcite obtuse steps during growth are revealed as a reduction in the obtuse-step spreading rate as well as rounding and roughening of such steps. Our results suggest that, together with changes in pH, variations in the calcification rate or the calcite crystallographic form in which boron is incorporated are important factors to consider when using boron in carbonates as a pH proxy, as these factors could also influence the amount of boron incorporated during growth and possibly the boron isotopic signature.