International guidance on bioanalytical method validation recommends the practice of partial validation when introducing a new matrix from the same species into a previously fully validated assay. Planning the partial validation protocol should include an evaluation of analyte chemistry, consideration of sample container materials, and a comparison of properties between the relevant biological matrices. Transition of a serum/plasma‐validated bioanalytical method to analysis from a low‐protein matrix, such as urine, cerebral spinal fluid, or oral fluid can result in inconsistent analyte recovery. The low recovery can potentially be mistaken for signal suppression or lack of drug stability and may be more pronounced in low‐concentration or low‐volume samples. In addition, adsorption and absorption interactions with containers may be exacerbated in low‐protein matrices. Several possibilities exist for mitigating the impact of non‐specific binding and low‐protein matrices, including surfactants, bovine serum albumin, and β‐cyclodextrin. Finally, higher matrix protein can facilitate analyte stability. Given all this, matrix protein content should not be overlooked when anticipating a partial bioanalytical method validation.