Jellies are usually preserved by artificial preservatives where they have harmful side effects and health hazards especially to infants. Honey and fresh lemon extract juice is a natural preservative and is considered a good substitute for artificial preservative. Due to increasing level of demand regarding health concern issue safe food, an attempt has undertaken to formulate the artificial preservative free guava–pineapple jelly and their marketability, physicochemical, bioactive compounds, microbial and antioxidant properties analysis during storage. In this study, the jelly was formulated using artificial preservative potassium metabisulphite (KMS) (T1), natural preservative honey and fresh lemon extract juice (T2 and T3), without artificial and natural preservative (T4) using different proportion of guava–pineapple extracted juice. Results of different treated jelly showed that T2 and T3 jelly was nutritionally superior. Bioactive compounds and antioxidant properties was highly present in T2 and T3 jelly. The brightest color (L* and C*) and highest hue angle (H*) value was noted in honey and fresh lemon extract juice treated jelly T2 and T3 upto 8 months of storage but after 9 months, darkest color was noted gradually. The consumer acceptance was extended to honey and lemon extract juice treated jelly (T2 and T3) for their impressive color and flavor. High incidence of microbial load was recorded in preservative free (both natural and artificial) jelly (T4). Low incidence of microbial load obtained from this study gives an indication that T2 and T3 jelly is microbiologically safe as natural jelly. Shelf life of natural preservative treated jelly (T2 and T3) could be extended upto 8 months and artificial preservative treated jelly could be upto 9 months (T1) at ambient condition without any quality deterioration. Overall, honey and fresh lemon extract juice are valuable source of natural preservative for formulation of fruit jelly. The processors could process and preserve the fruit jelly with decent aroma by applying this technology as an alternative to artificial food additives.