There is limited information on the effect of organic fertilizers on seed germination and subsequent transplant growth. The objective of this study was to determine the effects of application rate of blood meal (BM) and feather meal (FM) fertilizers on germination of tomato seeds. Both organic fertilizers were applied as amendments to peat-based organic substrates at rates ranging from 0 to over 50 g·kg−1 N. Tomato ‘Brandywine’ seed were sown in trays. Seed germination was recorded daily until the germination percentage remained unchanged. Ammonia concentration in the substrates (Pro-Mix and Miracle-Gro) increased with increasing rate of substrate N concentration. Ammonia concentration also increased with increasing time after incorporation of BM and FM reaching maximum values (16 ppm) at day 9. Tomato seed germination was little affected at BM and FM rates lower than ≈3 g·kg−1 N (4% w/w for BM or FM), but declined above 3 g·kg−1 N reaching 0% germination rate at ≈14 g·kg−1 N for both BM and FM. Substrates pH was 5.9 in the absence of BM or FM and increased to about pH 7 with addition of low rates of BM (2.7 g·kg−1 N) and FM (2.6 g·kg−1 N). Substrate electrical conductivity (EC) increased with increasing substrate N concentration as supplied by BM and FM; FM, however, had a stronger effect on increasing EC compared with BM. In conclusion, BM and FM had inhibitory effects on tomato seed germination when applied at more than 3 g·kg−1 N (4% w/w for BM or FM). High ammonia concentration in the substrates for the first 2 weeks after incorporation of BM or FM likely caused, at least partially, inhibition of tomato seed germination. Thus, substrate mixed with BM or FM should be allowed to incubate for at least 2 weeks before planting tomato seed.