Self‐assembled monolayers (SAMs) of oligoethylene glycol (OEG)‐terminated alkanethiolates on gold, which are used to control protein adsorption and cell adhesion, were patterned by reaction with Br2/HOBr electrogenerated at a microelectrode of a scanning electrochemical microscope (SECM). The spreading of the Br2 diffusion layers was limited by a homogeneous reaction with cystamine or L‐cystine as scavengers. The influence of process parameters on the patterning process was explored by simulation and combinatorial experiments. The experimental determination of pattern sizes from SECM feedback images was verified by scanning force microscopy. The simulation considered the local Br2 formation as well as Br2 consumption in the reaction with the OEG SAM, by reduction at the gold substrate, and by the homogeneous scavenging reaction. It used experimentally determined diffusion coefficients and rate constants of the scavenging reaction. and Experiments and simulation confirmed the existence of regions in the parameter space, in which the patterning process is robust against small variation of the parameters working distance, pulse time and scavenger excess.