A new kind of solid phase extraction (SPE), which we named in situ surfactant-based solid phase extraction (ISS-SPE), represents a simple, selective and rapid method for preconcentration and determination of manganese from food and water samples. This method has distinct advantages: extraction times are short and recoveries are high; further, we can see formation of fine particles of large specific surface and their good dispersion in the solution. In this work, a small amount of cationic surfactant, n-dodecyltrimethylammonium bromide (DTAB) was injected into the water sample containing Mn ions, which were complexed by 1-(2-pyridylazo)-2-naphthol (PAN). After shaking, a little volume of NaPF6 as an ion-pairing agent was added into the solution by a microsyringe. After preconcentration, the settled phase was dissolved in a specific volume of ethanol and then aspirated into the flame atomic absorption spectrometer by using a homemade microsample introduction system. The effective parameters such as pH, concentration of surfactant, concentration of chelating agent, concentration of ion-pairing agent and effect of salt concentration were optimized by a fractional factorial design to identify the most important parameters and their interactions, and central composite methodology was used to achieve the optimum point of effective parameters to the response. Under the optimum conditions, preconcentration of 10 ml of the sample solution permitted detection of 0.88 μg l−1 with enhancement factor of 45.6, and the relative standard deviation (RSD) for five determinations of Mn ions was 3.5%. The developed method was applied to the determination of trace manganese in various real samples with satisfactory results.