As can be expected where a dog is the real star of the film, animal action is throughout. In addition to the trained dogs who worked in the film, a full mechanical dog was also used, plus a mechanical dog's head which was used to achieve certain facial expressions and reactions. American Humane was on the set throughout filming. Prior to filming, AHA monitored training and preparation of the dogs for certain tricks that they had to master.

An opening scene establishes the gloomy laboratory where Varnick stows his stolen canines. When the puppies are stolen from the pet shop, they are put into cages in the back of a van. When the truck goes over a bump, a cage opens and Sparky, a clever little terrier, goes to Beethoven's cage and lifts the lever with his paw, letting Beethoven out. Sparky then goes to the back door of the truck, opens the latch on that door, and the two pups jump out of the rear of the moving van. This scene was shot in cuts. Trick camera angles were used to give the effect of the dogs escaping directly onto the street. For filming, the van moved very slowly as the dogs jumped approximately two feet to a platform that was attached to the back of the van. Separate shots were taken of the dogs' paws hitting the pavement. To get this, the dogs were dropped into the shot by the trainers from a height of approximately three feet.

As the St. Bernard pup embarks on his adventure he meets his first cat, who hisses and swats at him. This scene was shot in cuts. The cat was held in place on a mark by way of a tie-down and the dog was walked A to B on a leash towards the cat. The cat reacted to the dog by hissing and swatting. He next meets a gardener who is sweeping leaves with a leaf blower and the pup is also blown. The pup reacted primarily to the sound of the blower as only a small amount of air was blown on him.

Once a part of the Newton family, Beethoven has his share of misadventures, such as when he drinks out of a fish bowl while the fish are swimming in it. To film this the dog was allowed to drink for about two seconds with the trainers close by off camera in case the dog got too close to the fish. Beethoven also shares in many of the activities of the children. When they dress up for Halloween, Beethoven also dresses as a horse, complete with a miniature saddle. Beethoven shares in many food treats, sometimes offered to him, sometimes stolen. During filming the dog would only take the food upon his trainers cue. Beethoven plays cupid for Ryce by taking a stick to a boy and bringing the boy back to Ryce. This was accomplished by the dog responding to his trainer's verbal and hand cues.

Sparky is dognapped while he is out helping his homeless master collect aluminum cans. Sparky follows an aluminum can that is being pulled on a string and a net is thrown over him. This scene was shot in cuts. The can was being pulled by the trainer and the net was placed very carefully over the dog by another trainer.

When Beethoven goes to the vet's to get his shots, he is placed on an examining table. He sees the nurse come in with a large syringe. When Beethoven looks at the syringe his eyes bulge. This expression was accomplished with the help of a mechanical dog head. When the nurse holds up the needle in the foreground we see a slightly out of focus Beethoven fall over and faint in the background. The "dog" in the background was actually a man in a dog suit.

Alice goes back to work and leaves the children in the care of a baby-sitter. While Ted and Ryce are in the house with the baby-sitter, the youngest, Emily, plays ball outside near the pool. Emily reaches for the ball that has gone into the pool and she tumbles into the water. Her screams can't be heard by the other children and the baby-sitter, who is noisily entertaining them, but Beethoven hears. He escapes his fenced enclosure, by way of a ditch he has dug, and races to Emily's rescue, jumping over a tall fence and diving into the pool where he rescues Emily. This scene was shot in many cuts. The dog first escaped his run by crawling through a ditch that had been dug under the fence. The jump over the fence was accomplished by the dog jumping about two and a half feet over the camera. At a different time the dog was filmed making a broad jump from one platform to another. The dog had been pre-conditioned and trained for this jump. For the shot of the dog diving into the pool the trainers actually dropped the dog into the pool and the takes were kept to a minimum of three. Other shots were taken of the dog swimming from various angles. The dog would be released from one edge of the pool and called to the other by his trainer. For the shot in which Emily climbs onto Beethoven and rides him out of the pool, a man in a dog suit was actually used. When using the real dog, care was taken so that he would not tire. A mechanical dog was also used in addition to the man in the dog suit to keep both the child and the real dog from being injured or scratched.

George brings home important clients for a barbecue and while George is inside Beethoven overhears the couple discussing how they are going to swindle George out of his company. While the couple are seated around a patio table, Beethoven, on a very long leash, encircles the pair. When a ball is thrown over a fence Beethoven chases after it, dragging the couple with him. When he sees a cat, he takes off after the cat, dragging the couple back and forth. This scene was shot in cuts. A ramp was used for the dog jumping over the fence. The dog jumped approximately two feet. The table and chairs with the couple sitting in them were rigged with a cable attached to a truck which pulled them. The dog ran alongside the cable, but camera angles made it appear as if he was dragging the couple and the table.

When Dr. Varnick arrives at the Newton home to stage his phoney dog attack, he smears fake blood on Beethoven's nose and his own arm. A harmless, non-toxic make-up was used for this. For the phoney dog attack the trainer was a photo double for the actor and merely played with the dog. A man in a dog costume was also used in part of this scene.

After George turns over Beethoven to Varnick, Varnick has his two goons, Harvey and Vernon, transfer Beethoven to his laboratory by way of a van. Beethoven is muzzled and removed from the van by way of a come-along device consisting of a snare at the end of a pole and Beethoven resists the entire time. The trainer was a photo double for the actor and held the pole, which was attached to a special dog collar. The collar was 2 inches wide and covered with fake fur to match the dog's fur so that no pressure would be put on his neck when he was in the come-along. A man in a dog costume was also used for any violent action with the come-along snare. Although the snare appeared to jerk the dog, the dog was reacting to his trainer's voice and no pressure of any significance was applied with the come-along. Once inside the lab Beethoven sees his old pal, Sparky. When Varnick sends Harvey and Vernon to the lab to fetch Beethoven and Sparky to begin his experiments, Beethoven is again ensnared in the come-along device. Again, this was done as explained previously. Sparky is picked up by the scruff of his neck. To accomplish this the actor was meticulously rehearsed by the trainer using a toy dog before using the actual dog. The dog playing Sparky was conditioned to be handled by the scruff of the neck.

Simultaneously, George breaks into the lab just in time to distract Varnick and his goons. Beethoven breaks free and Sparky leaps up and attacks Varnick, biting into his crotch. When Varnick finally gets Sparky to release his hold he throws Sparky against a wall. This was accomplished by the trainer doubling for the actor. The dog went for a toy that was attached to the trainer's crotch. When Sparky was thrown against the wall, he was actually tossed by one trainer into a blanket about three feet away that was held by two other trainers. All of this action was shot in cuts. When Beethoven rushes to help George fight off Vernon and Harvey, in the struggle that ensues, the trainer doubled for the actor and actually played with the dog to simulate a struggle. Alice and the children come to the rescue of George and the dogs by crashing the family station wagon through the wall of the laboratory. When the car actually came through the wall, the real dogs in the dog cages were replaced with fake dogs. After the scene with the car coming through the wall was complete, the real dogs were then put back in the cages. The Newton family begins to free all the dogs from their cages. The freed dogs chase Vernon and Harvey down the street and through a produce market to a dead end where they come to a chain-link fence. They successfully scale the fence and think that they have evaded the pack of pursuing pooches only to discover that they are now face to face with four Doberman guard dogs who stand growling menacingly.

The above scenes were shot in many cuts. As the dogs are freed and jumped from their cages they jumped onto a floor that was padded with stunt mats and a large holding pen was used to receive the dogs off camera as they ran to the trainers who were calling them. For the chase scene the trainers would entice the dogs with their favorite toys or call them with verbal and hand commands. It was all just a game to the dogs. Portable pens were established at the end of the run with several trainers there to herd the dogs and keep them in control. As the dogs ran through the market, chicken wire was set up along the edge of the route from point A to point B to keep dogs from straying the wrong way. The Dobermans barked and growled in response to their trainer's hand signals.