The interrelationships between silage preference of ruminants and compounds that may affect dry matter (DM) intake (DMI) are not yet fully enlightened. Metabolic studies in addition to conventional chemical analysis and preference trials provided new insights. Six silage treatments each of alfalfa (ALF) and red clover (RC) with different DM (222–391 g/kg), silage additives and intended addition of soil were produced to obtain a range of qualities. After 120 d of ensiling, silages were sampled for chemical analysis, vacuum-packed and refrigerated for subsequent preference trials with goats. Within 21 d, each possible combination of 2 silages (n = 21) was presented for 3 h for ad libitum intake to goats (Saanen-type wethers, n = 8, body weight 105 ± 2.7 kg). The mean value comparisons (3 h DMI) were made using a variance analysis including terms for treatment and animal and the Waller-Duncan k-ratio t-test to separate means (SAS 9.3). Although treatments led only to few differences in fermentation acids and crude protein composition, preference behavior was strongly divergent. The most preferred and avoided treatments of ALF and RC silage amounted to 863, 858, 226, and 282 g DMI/3 h, respectively. Fermentation acid analysis showed the most obvious differences in acetic acid. To further explore relations between preference and silage composition a metabolome analysis was implemented. Metabolites (all low molecular weight molecules) were analyzed by a non-targeted metabolite profiling in the range of 50–1,700 Da. In 2 treatments of each plant species (those which were most different in preference) more than 6,400 compounds were detected and 2,010 were identified. For an initial overview of all analyzed samples a principal component (PC) analysis (PCA) was conducted: PC 1 clearly separated the different plant species, explaining 40.7% of all variances in the data set; PC2 separated the silage treatments explaining 22.9% of all variances. Between preferred and avoided treatments 934 compounds differed in RC and 1,860 in ALF. 475 of those were altered in both plant species (251 were reduced and 186 were increased; only 38 behaved contrarily). The database provides a useful foundation for the approach of explaining silage intake behavior by ruminants.