This paper presents a comparative investigation of recovery procedures for the analysis of natural organic colorants, encompassing ten major natural organic dye chemical classes, several sample types (silk, wool, cotton, pigment, paint), prepared from the extracts of twelve biological sources, and nine different recovery protocols. These protocols are based on the traditional harsh hydrochloric acid method; on mild hydrolysis methods involving formic, oxalic or hydrofluoric acid; and on methods consecutively employing mild and harsh hydrolysis on the same sample. An evaluation system was developed by classifying analytical results in an upper, middle or lower grade with reference to the best result obtained. This classification was used to calculate scores for each hydrolysis method and for either textile (silk and wool or cotton) or pigment/paint. The best overall hydrolysis method for textile samples was a combination of mild oxalic acid with traditional hydrochloric acid hydrolysis. The best overall hydrolysis method for pigment/paint was a combination of a newly modified mild hydrofluoric acid treatment with traditional hydrochloric acid hydrolysis. The application of these methods to historical samples will not necessarily give the optimal result achievable for every biological source, but will definitely reduce the risk of missing essential information for the elucidation of ancient technology in a geographical and historical context. The reduced level of risk will avoid repetitive sampling and reduce the level of invasiveness, hence taking into account good conservation policies. The potential of these selected methods is illustrated with the analysis of some historical Chinese textile and paint samples.