Provided are systems and methods for adapting to volume variations in microfluidic chromatography columns. A column is calibrated by comparing a parameter of the column with a same parameter of a reference column and generating, by a processor, an adjustment factor in response to the comparison between the parameter of the column with a same parameter of the reference column. Volume differences between the calibrated column and the reference column are compensated for by integrating the generated adjustment factor into a sample separation involving the calibrated column.