© 2015 ESO. Aims. We present MUFFIT, a new generic code optimized to retrieve the main stellar population parameters of galaxies in photometric multi-filter surveys, and check its reliability and feasibility with real galaxy data from the ALHAMBRA survey. Methods. Making use of an error-weighted ξ2-test, we compare the multi-filter fluxes of galaxies with the synthetic photometry of mixtures of two single stellar populations at different redshifts and extinctions, to provide the most likely range of stellar population parameters (mainly ages and metallicities), extinctions, redshifts, and stellar masses. To improve the diagnostic reliability, MUFFIT identifies and removes from the analysis those bands that are significantly affected by emission lines. The final parameters and their uncertainties are derived by a Monte Carlo method, using the individual photometric uncertainties in each band. Finally, we discuss the accuracies, degeneracies, and reliability of MUFFIT using both simulated and real galaxies from ALHAMBRA, comparing with results from the literature. Results. MUFFIT is a precise and reliable code to derive stellar population parameters of galaxies in ALHAMBRA. Using the results from photometric-redshift codes as input, MUFFIT improves the photometric-redshift accuracy by ∼10-20%. MUFFIT also detects nebular emissions in galaxies, providing physical information about their strengths. The stellar masses derived from MUFFIT show excellent agreement with the COSMOS and SDSS values. In addition, the retrieved age-metallicity locus for a sample of z ≤ 0.22 early-type galaxies in ALHAMBRA at different stellar mass bins are in very good agreement with the ones from SDSS spectroscopic diagnostics. Moreover, a one-to-one comparison between the redshifts, ages, metallicities, and stellar masses derived spectroscopically for SDSS and by MUFFIT for ALHAMBRA reveals good qualitative agreements in all the parameters, hence reinforcing the strengths of multi-filter galaxy data and optimized analysis techniques, like MUFFIT, to conduct reliable stellar population studies. ; We thank the referee for the valuable suggestions and comments that reinforced part of our results. L.A.D.G. acknowledges support from the >Caja Rural de Teruel> for developing this research. A.J.C. is a Ramon y Cajal Fellow of the Spanish Ministry of Science and Innovation. This work has been supported by the >Programa Nacional de Astronomia y Astrofisica> of the Spanish Ministry of Economy and Competitiveness (MINECO) under grant AYA2012-30789, as well as by FEDER funds and the Government of Aragon, through the Research Group E103. L.A.D.G. also thanks the Mullard Space Science Laboratory (MSSL) and Royal Astronomical Society (RAS) for offering the opportunity to support and develop part of this research in collaboration with I.F. MINECO grants AYA2010-15081, AYA2010-15169, AYA2010-22111-C03-01, AYA2010-22111-C03-02, AYA2011-29517-C03-01, AYA2013-40611-P, AYA2013-42227-P, AYA2013-43188-P, AYA2013-48623-C2-1, AYA2013-48623-C2-2, and AYA2014-58861-C3-1 are also acknowledged, together with Generalitat Valenciana projects Prometeo 2009/064 and PROMETEOII/2014/060, and Junta de Andalucia grants TIC114, JA2828, and P10-FQM-6444. MP acknowledges financial support from the JAE-Doc programme of the Spanish National Research Council (CSIC), co-funded by the European Social Fund. ; Peer Reviewed