In this work, novel bone substitutes in the form of biomicroconcretes with high surgical handiness and satisfactory mechanical properties were developed. Materials were composed of hybrid hydroxyapatite/chitosan (HAp/CTS) granules as aggregate, α-TCP as a setting phase, and pectin solutions as a liquid phase. Two types of low esterified amidated pectins from citrus peels (CP) and apple pomace (AP) and also two fractions of HAp/CTS granules of size between 300 and 400 µm and 400–600 µm were used. The presence of pectins significantly improved surgical handiness and allowed to obtain injectable biomicroconcretes. Synergistic effect of fast internal crosslinking of low esterified pectins, induced by Ca2+ released from α-TCP, together with setting reaction of highly reactive α-TCP (dual setting system) resulted in excellent cohesion of the final materials. By the use of different type of pectins (AP, CP) one can control mechanical properties of the materials. The results showed that pectins from citrus peels more effectively improved compressive strength. The biomicroconcretes obtained in this work showed great potential for the use as novel bone substitutes, however, they require further studies, especially biological evaluation.