documentclass{article}

usepackage{fontspec}
setmainfont{FreeSerif.otf}

% turn on xetex character class feature
XeTeXinterchartokenstate=1

% character class for beta
newXeTeXintercharclassmyc

% assign beta to the class
XeTeXcharclass`β=myc

% specify that swapbeta should be inserted between any
% normal character (class zero) and a beta (class mych)
XeTeXinterchartoks 0 myc{swapbeta}

% define swapbeta to swallow a β and expand to ϐ
defswapbeta β{ϐ}

% To do the same for phi just define a new class and a new swapphi
% command and set up a substitution for that.

 % testing...
begin{document}

 abc βέβα

end{document}