An experiment was conducted to determine the accumulation of trace metals, zinc (Zn), chromium (Cr), manganese (Mn) and iron (Fe), in three types of arable soils (Brown Lowland soil, Andosol and Brown Forest soil) amended with chemical fertilizers (CHF), cattle farmyard manure (CFM) and pig farmyard manure (PFM) over a 5-year period. Two methods were used to determine the total amount of trace metals: the instrumental neutron activation analysis (INAA), as a non-destructive measurement, and the concentrated acid digestion method (CADM), as a destructive measurement. Results of soil analyses using both INAA and CADM indicated that PFM application resulted in a considerable increase in the amount of Zn in arable soils compared with CHF application, unlike CFM application. Results obtained from the two methods were not fully in agreement for Cr. Based on INAA, soil accumulation of Cr from CFM and PFM applications was not significant in any soil type. In contrast, based on CADM, Cr accumulation was relatively higher in the Brown Forest soil with PFM than with CHF application. The soil types and treatments exerted various effects on Cr, Mn and Fe concentrations. The 5-year application of animal manure did not result in a considerable increase in Cr, Mn and Fe concentrations in soils, whereas longer-term application may lead to a gradual accumulation of Cr and Fe depending on the soil and manure types. The use of CADM in the present study may not always be adequate to assess the accumulation of trace metals in soils amended with CFM and PFM because of the conditions of the measurements, such as sensitivity, dilution level or type of instrument, and not because of the digestion method. The types of soil and manure affect trace metal accumulation in arable soils, and elements in the manure relate to the ability of soils to retain trace metals. It is important that the results of non-destructive and destructive measurements, obtained using INAA and CADM, be evaluated properly.